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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.

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At least 433 records · Page 24
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Structural and physical features that distinguish tumor-controlling from inactive cancer neoepitopes

Neoepitopes arising from amino acid substitutions due to single nucleotide polymorphisms are targets of T cell immune responses to cancer and are of significant interest in the development of cancer vaccines. However, understanding the characteristics of rare protective neoepitopes that truly control tumor growth has been a challenge, due to their scarcity as well as the challenge of verifying true, neoepitope-dependent tumor control in humans. Taking advantage of recent work in mouse models that circumvented these challenges, here, we compared the structural and physical properties of neoepitopes that range from fully protective to immunologically inactive. As neoepitopes are derived from self-peptides that can induce immune tolerance, we studied not only how the various neoepitopes differ from each other but also from their wild-type counterparts. We identified multiple features associated with protection, including features that describe how neoepitopes differ from self as well as features associated with recognition by diverse T cell receptor repertoires. In conclusion, we demonstrate both the promise and limitations of neoepitope structural analysis and predictive modeling and illustrate important aspects that can be incorporated into neoepitope prediction pipelines.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Catalytic CO Oxidation on MgAl 2 O 4 -Supported Iridium Single Atoms: Ligand Configuration and Site Geometry

Probing and understanding the local chemical environment of an active site is essential for designing high-performance single-atom catalysts (SACs). Density functional theory (DFT) calculations were performed to investigate the ligand configuration and site geometry of MgAl 2 O 4 -supported iridium single atoms (Ir-1) toward catalytic carbon monoxide (CO) oxidation. We employed MgAl 2 O 4 (111) and MgAl 2 O 4 (211) as the model substrates with adsorbed Ir single atoms of different site geometries. DFT calculations revealed that the Mg-site on MgAl 2 O 4 (111) and the step site on MgAl 2 O 4 (211) are the most stable adsorption sites for Ir single atoms. Irrespective of site choices, CO oxidation on supported Ir single atoms follows the Eley-Rideal (E-R) mechanism, in which the surface oxygen vacancies close to the Ir single atoms activate molecular O 2 with a negligible barrier and the rate-limiting step is the gas-phase CO directly attacking the O-Ir species that is modulated by a CO ligand. Furthermore, first-principles X-ray absorption near-edge spectra of reaction intermediates along with in situ/operando X-ray absorption spectroscopy (XAS) suggest that Ir single atoms adsorb primarily on the step sites of MgAl 2 O 4 . However, microkinetic modeling predicts that a higher activity can be attained on the equally stable Mg-site, maximizing the population of which in catalyst synthesis might prove fruitful in future studies. Electronic structure analysis indicates that the CO ligand increases the reactivity of adsorbed oxygen atoms bound to Ir single atoms by increasing the antibonding nature of the O-Ir bond.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Impact of Cation Insertion on Semiconducting Polymer Thin Films toward Electrochemical Energy Conversion

Semiconducting polymers are being explored for electrochemical and photoelectrochemical energy transformation and storage applications. For these applications, it is critical to understand how ion insertion from the electrolyte into polymer electrodes modulates the polymer electronic structure and electron doping levels. Here, this study explores electrochemical cation insertion in the n-type conjugated redox polymer P90, composed of alternating naphthalene diimide (NDI) acceptor and bithiophene (T2) donor units, where the NDI units are functionalized with heptaethylene glycol (HEG, 90%) and 2-octyl dodecyl (OD, 10%) side chains. By combining in situ techniques (UV-vis absorption and Raman spectroscopies with electrochemistry), structural analysis using ex situ grazing-incidence wide-angle X-ray scattering (GIWAXS), and density functional theory (DFT) calculations, we reveal that dications enable negative polaron and bipolaron formation in the P90 at less reducing potentials while supporting more bipolaron formation than the monocations; moreover, larger dications with smaller hydrated radii increase the maximum P90 electron doping level. We also determine that the monocations lead to more thermodynamically stabilized polarons compared with the dications. These findings highlight the critical role of cation identity in tuning electrochemical charging, charge stabilization, and electronic structure of n-type conjugated redox polymers, providing guidance on the rational design of polymer-based (photo)electrochemical applications.

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

Structural basis for severe pain caused by mutations in the S4-S5 linkers of voltage-gated sodium channel Na V 1.7

Gain-of-function mutations in voltage-gated sodium channel Na V 1.7 cause severe inherited pain syndromes, including inherited erythromelalgia (IEM). The structural basis of these disease mutations, however, remains elusive. Here, we focused on three mutations that all substitute threonine residues in the alpha-helical S4-S5 intracellular linker that connects the voltage sensor to the pore: Na V 1.7/I234T, Na V 1.7/I848T, and Na V 1.7/S241T in order of their positions in the amino acid sequence within the S4-S5 linkers. Introduction of these IEM mutations into the ancestral bacterial sodium channel Na V Ab recapitulated the pathogenic gain-of-function of these mutants by inducing a negative shift in the voltage dependence of activation and slowing the kinetics of inactivation. Remarkably, our structural analysis reveals a common mechanism of action among the three mutations, in which the mutant threonine residues create new hydrogen bonds between the S4-S5 linker and the pore-lining S5 or S6 segment in the pore module. Because the S4-S5 linkers couple voltage sensor movements to pore opening, these newly formed hydrogen bonds would stabilize the activated state substantially and thereby promote the 8 to 18 mV negative shift in the voltage dependence of activation that is characteristic of the Na V 1.7 IEM mutants. Our results provide key structural insights into how IEM mutations in the S4-S5 linkers may cause hyperexcitability of Na V 1.7 and lead to severe pain in this debilitating disease.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Trickier than It Looks: Isomerization between Five- and Six-Coordinated Zinc in Heterometallic Li 2 Zn 2 Molecule

This report describes the synthesis and characterization of two hetero bi metallic Li–Zn coordination isomers [Li 2 Zn 2 (tbaoac) 6 ] (tbaoac = tert -butyl acetoacetato) that have been isolated separately by the same stoichiometric reaction run in different organic solvents. The 6-coordinated zinc isomer ( 6-Zn ) was synthesized in acetone with high yield, while the 5-coordinated one ( 5-Zn ) was readily obtained from ethanol. The 5-Zn isomer has a low solubility in organic solvents such as alkanes and haloalkanes, while its 6-Zn counterpart exhibits a good solubility in almost all common solvents. Two isomeric molecules feature similar centrosymmetric tetranuclear cyclic assemblies, which are different in their arrangement of tbaoac ligands. While all ligands act as μ 2 -type in the structure of 5-Zn , the two tbaoac groups chelating Li appear as μ 3 -type in 6-Zn , thus providing an additional coordination for Zn ions. However, the real structural transformation between these isomers was shown to be more complex than simply making or breaking a couple of Zn–O bonds. X-ray single-crystal structure analysis, powder X-ray diffraction, multinuclear NMR, DART mass spectrometry, ICP-OES analysis, and TGA have been employed for the characterization of the isomers. The combination of powder X-ray diffraction and 1 H NMR investigation revealed that 6-Zn isomer can be quantitatively transformed to 5-Zn in ethanol, while the reverse conversion instantly takes place in acetone.

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

Resolving metal binding properties within subunits of a multimeric enzyme Mnx by surface induced dissociation and native ion mobility mass spectrometry

Multi-subunit enzymes function as coordinated assemblies. Yet most enzymatic assays measure the summed output of all populations in solution and cannot easily differentiate contributions of individual subunits. Native mass spectrometry detects intact protein complexes in the gas phase. Surface induced dissociation further releases subunits from protein complexes while retaining compact conformations and bound ligands. Combined with ion mobility, the released subunits can then be carefully monitored for more in-depth structural analysis. Mnx is a unique bacterial multicopper oxidase complex that oxidizes Mn(II) to form MnO 2 minerals, and is composed of three subunits: MnxG, a multicopper oxidase containing the active site, and two accessory proteins, MnxE and MnxF which also bind copper ions. Other known multicopper oxidases do not require accessory proteins, therefore the functions of MnxE and MnxF are not well understood. Here, we use native mass spectrometry with surface induced dissociation and ion mobility to characterize the metal binding properties of Mnx with two metals, catalytic Cu(II) and Mn(II) substrate. We demonstrate our assay can detect subtle structural changes within each subunit, which are presumably related to the allosteric mechanism. We also noticed that ionic strength and solution composition can impact metal binding and must be carefully investigated for such experiments.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Genomic analysis and identification of a novel superantigen, SargEY, in Staphylococcus argenteus isolated from atopic dermatitis lesions

During surveillance of Staphylococcus aureus in lesions from patients with atopic dermatitis (AD), we isolated Staphylococcus argenteus, a species registered in 2011 as a new member of the genus Staphylococcus and previously considered a lineage of S. aureus. Genome sequence comparisons between S. argenteus isolates and representative S. aureus clinical isolates from various origins revealed that the S. argenteus genome from AD patients closely resembles that of S. aureus causing skin infections. We previously reported that 17%–22% of S. aureus isolated from skin infections produce staphylococcal enterotoxin Y (SEY), which predominantly induces T-cell proliferation via the T-cell receptor (TCR) Vα pathway. Complete genome sequencing of S. argenteus isolates revealed a gene encoding a protein similar to superantigen SEY, designated as SargEY, on its chromosome. Population structure analysis of S. argenteus revealed that these isolates are ST2250 lineage, which was the only lineage positive for the SEY-like gene among S. argenteus. Recombinant SargEY demonstrated immunological cross-reactivity with anti-SEY serum. SargEY could induce proliferation of human CD4 + and CD8 + T cells, as well as production of TNF-α and IFN-γ. SargEY showed emetic activity in a marmoset monkey model. S arg EY and SET (a phylogenetically close but uncharacterized SE) revealed their dependency on TCR Vα in inducing human T-cell proliferation. Additionally, TCR sequencing revealed other previously undescribed Vα repertoires induced by SEH. S arg EY and SEY may play roles in exacerbating the respective toxin-producing strains in AD.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

The pectin puzzle: Decoding the fine structure of rhamnogalacturonan-I (RG-I) in Arabidopsis thaliana uncovers new pectin features

Pectin is generally divided into four distinct structural categories, namely homogalacturonan, xylogalacturonan, rhamnogalacturonan I (RG-I) and rhamnogalacturonan II. While much of the structural diversity of homogalacturonan, xylogalacturonan and rhamnogalacturonan II has been elucidated, the structural features of RG-I are less well understood. In this work, we employed multiple complementary analytical techniques to present a detailed structural analysis of RG-I in the model species Arabidopsis thaliana . Starting with highly purified RG-I from different Arabidopsis tissues, we employed comparative linkage and nuclear magnetic resonance analysis along with mass spectrometry analysis of enzymatically digested RG-I oligosaccharides. Besides the presence of the canonical α-1,5-arabinan, β-1,4-galactan, β-1,6-galactan and arabinogalactan RG-I side chains of varying lengths, we show that a large portion of the β-1,6-galactan is terminated by either 4-O-methyl β-glucuronic acid (GlcA) residues or, to a smaller degree, β-GlcA that lacks the Me-ether group. Importantly, O-acetylation of RG-I GalA residues is a minor modification while 10 % of the backbone Rha residues are 3-O-acetylated, and most of the acetylated Rha is additionally branched with β-galactose substituents. Taken together, the combined results of these different analytical techniques present the most comprehensive structural overview of Arabidopsis thaliana RG-I to date.

25 ENERGY STORAGE↗
DOE OSTI2023

Emerging Two-Dimensional Organic Semiconductor-Incorporated Perovskites–A Fascinating Family of Hybrid Electronic Materials

Halide perovskites have attracted a great amount of attention owing to their unique materials chemistry, excellent electronic properties, and low-cost manufacturing. Two-dimensional (2D) halide perovskites, originating from three-dimensional (3D) perovskite structures, are structurally more diverse and therefore create functional possibilities beyond 3D perovskites. The much less restrictive size constraints on the organic component of these hybrid materials particularly provide an exciting platform for designing unprecedented materials and functionalities at the molecular level. In this Perspective, we discuss the concept and recent development of a sub-class of 2D perovskites, namely, organic semiconductor-incorporated perovskites (OSiPs). OSiPs combine the electronic functionality of organic semiconductors with the soft and dynamic halide perovskite lattice, offering opportunities for tailoring the energy landscape, lattice and carrier dynamics, and electron/ion transport properties for various fundamental studies, as well as device applications. Specifically, we summarize recent advances in the design, synthesis, and structural analysis of OSiPs with various organic conjugated moieties as well as the application of OSiPs in photovoltaics, light-emitting devices, and transistors. As a result, challenges and further opportunities for OSiPs in molecular design, integration of novel functionality, film quality, and stability issues are addressed.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Warm Unit Stand Analysis for Proton Improvement Project II

The Proton Improvement Project II, commonly referred to as PIP II, is a linear accelerator overhaul at Fermilab to eventually double the output of its existing proton beam to continue to be the leading force in high energy physics. The proton beam is created through a series of high frequency cryomodules that must be connected utilizing a combination of magnets and vacuum pumps to ensure the beam is properly aligned. A housing mechanism for the magnets and vacuum pumps (Warm Units) will be placed between the cryomodules for realignment and require multiple stages of 6 degree-of-freedom adjustment options, to ensure that the beam alignment can fit all realistic requirements. Extensive testing and design modifications on the Warm Unit stand was completed to confirm not only the strength of the unit in nominal configuration, but also at each possible adjustment orientation for each 6 degree-of-freedom option. Structural analysis was also completed for various unique loading conditions i ncluding transportation loading and confirming the unit satisfies international building code. Simultaneously, testing and design modifications were done to confirm that the frequency modes of the system resided outside of concern ranges, which is determined by Fermilab safety codes and is set to exceed 15 Hz. Design changes that simultaneously stiffen the system to raise the lowest frequency modes while expanding access for technicians and allow for easier fabrication were developed and implemented into the Warm Unit stand. Various relationships between the design changes and the overall vibrational patterns were also developed for future use and study as the rest of PIP II matures.

43 PARTICLE ACCELERATORS↗
DOE OSTI2022

PplD is a de-N-acetylase of the cell wall linkage unit of streptococcal rhamnopolysaccharides

The cell wall of the human bacterial pathogen Group A Streptococcus (GAS) consists of peptidoglycan decorated with the Lancefield group A carbohydrate (GAC). GAC is a promising target for the development of GAS vaccines. In this study, employing chemical, compositional, and NMR methods, we show that GAC is attached to peptidoglycan via glucosamine 1-phosphate. This structural feature makes the GAC-peptidoglycan linkage highly sensitive to cleavage by nitrous acid and resistant to mild acid conditions. Using this characteristic of the GAS cell wall, we identify PplD as a protein required for deacetylation of linkage N-acetylglucosamine (GlcNAc). X-ray structural analysis indicates that PplD performs catalysis via a modified acid/base mechanism. Genetic surveys in silico together with functional analysis indicate that PplD homologs deacetylate the polysaccharide linkage in many streptococcal species. We further demonstrate that introduction of positive charges to the cell wall by GlcNAc deacetylation protects GAS against host cationic antimicrobial proteins.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Pnictogen Bonding at the Core of a Carbene-Stiborane-Gold Complex: Impact on Structure and Reactivity

Our interest in the design of ambiphilic ligands and their coordination to gold has led us to synthesize an indazol-3-ylidene gold chloride complex functionalized at the 4-position of the indazole backbone by a stibine functionality. The antimony center of this new complex cleanly reacts with o-chloranil to afford the corresponding stiborane derivative. Structural analysis indicates that the stiborane coordination environment is best described as a distorted square pyramid whose open face is oriented toward the gold center, allowing for the formation of a long donor–acceptor, or pnictogen, Au → Sb bonding interaction. The presence of this interaction, which has been probed computationally, is also manifested in the enhanced catalytic activity of this complex in the cyclization of N-propargyl-4-fluorobenzamide.

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

Structural and functional validation of a highly specific Smurf2 inhibitor

Smurf1 and Smurf2 are two closely related member of the HECT (homologous to E6AP carboxy terminus) E3 ubiquitin ligase family and play important roles in the regulation of various cellular processes. Both were initially identified to regulate transforming growth factor‐β and bone morphogenetic protein signaling pathways through regulating Smad protein stability and are now implicated in various pathological processes. Generally, E3 ligases, of which over 800 exist in humans, are ideal targets for inhibition as they determine substrate specificity; however, there are few inhibitors with the ability to precisely target a particular E3 ligase of interest. In this work, we explored a panel of ubiquitin variants (UbVs) that were previously identified to bind Smurf1 or Smurf2. In vitro binding and ubiquitination assays identified a highly specific Smurf2 inhibitor, UbV S2.4, which was able to inhibit ligase activity with high potency in the low nanomolar range. Orthologous cellular assays further demonstrated high specificity of UbV S2.4 toward Smurf2 and no cross‐reactivity toward Smurf1. Structural analysis of UbV S2.4 in complex with Smurf2 revealed its mechanism of inhibition was through targeting the E2 binding site. In summary, we investigated several protein‐based inhibitors of Smurf1 and Smurf2 and identified a highly specific Smurf2 inhibitor that disrupts the E2–E3 protein interaction interface.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Structures of drug-specific monoclonal antibodies bound to opioids and nicotine reveal a common mode of binding

Opioid-related fatal overdoses have reached epidemic proportions. Because existing treatments for opioid use disorders offer limited long-term protection, accelerating the development of newer approaches is critical. Monoclonal antibodies (mAbs) are an emerging treatment strategy that targets and sequesters selected opioids in the bloodstream, reducing drug distribution across the blood-brain barrier, thus preventing or reversing opioid toxicity. We previously identified a series of murine mAbs with high affinity and selectivity for oxycodone, morphine, fentanyl, and nicotine. To determine their binding mechanism, we used X-ray crystallography to solve the structures of mAbs bound to their respective targets, to 2.2 Å resolution or higher. Structural analysis showed a critical convergent hydrogen bonding mode that is dependent on a glutamic acid residue in the mAbs’ heavy chain and a tertiary amine of the ligand. Further, characterizing drug-mAb complexes represents a significant step toward rational antibody engineering and future manufacturing activities to support clinical evaluation.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Atomic-Scale View of Redox Induced Changes for Monolayer MoO x on α-TiO 2 (110) with Chemical-State Sensitivity

Supported molybdenum oxide (MoO x ) plays an important role in catalytic transformations from alcohol dehydrogenation to transesterification. During these reactions, Mo and oxygen surface species undergo structural and chemical changes. A detailed, chemical-state specific, atomic-scale structural analysis of the catalyst under redox conditions is important for improving catalytic properties. In this study, monolayer of MoO x grown on α-TiO 2 (110) by atomic-layer deposition is analyzed by X-ray standing wave (XSW) excited X-ray photoelectron spectroscopy (XPS). The chemical shifts for Mo 2p 3/2 and O 1s peaks are used to distinguish Mo 6+ from Mo 4+ and surface O from bulk O. Excitation of XPS by XSW allows pin-pointing the location of these surface species relative to the underlying substrate lattice. Finally, measured 3D composite atomic density maps for the oxidized and reduced interfaces compare well with our density functional theory models, and collectively create a unique view of the redoxdriven dynamics for this complex catalytic structure.

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

Ground and excited electronic structures of electride and alkalide units: The cases of Metal-Tren, -Azacryptand, and -TriPip222 complexes

A systematic electronic structure analysis was conducted for M(L) n molecular electrides and their corresponding alkalide units M(L) n @M' (M/M' = Na, K; L = Tren, Azacryptand, TriPip222; n = 1, 2). All complexes belong to the “superalkali” category due to their low ionization potentials. The saturated molecular electrides display M+(L) n - form with a greatly diffuse quasispherical electron cloud. They were identified as “superatoms” considering the contours of populating atomic-type molecular orbitals. The observed superatomic Aufbau order of M(Tren) 2 is 1S, 1P, 1D, 1F, 2S, 2P, and 1G and it is consistent with those of M(Azacryptand) and M(TriPip222) up to the analyzed 1F level. Their excitation energies decrease gradually moving from M(Tren) 2 to M(Azacryptand) and to M(TriPip222). The studied alkalide complexes carry [M(L) n ] + @M' - ionic structure and their dissociation energies vary in the sequence of K(L) n @Na > Na(L) n @Na > K(L) n @K > Na(L) n @K. Similar to molecular electrides, the anions of alkalide units occupy electrons in diffuse Rydberg-like orbitals. In this work, excited states of [M(L) n @M'] 0/+/- and their trends are also analyzed.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Insights into the κ/ι-carrageenan metabolism pathway of some marine Pseudoalteromonas species

Pseudoalteromonas is a globally distributed marine-associated genus that can be found in a broad range of aquatic environments, including in association with macroalgal surfaces where they may take advantage of these rich sources of polysaccharides. The metabolic systems that confer the ability to metabolize this abundant form of photosynthetically fixed carbon, however, are not yet fully understood. Through genomics, transcriptomics, microbiology, and specific structure-function studies of pathway components we address the capacity of newly isolated marine pseudoalteromonads to metabolize the red algal galactan carrageenan. The results reveal that the κ/ι-$\underline{car}$rageenan specific $\underline{p}$olysaccharide utilization $\underline{l}$ocus (CarPUL) enables isolates possessing this locus the ability to grow on this substrate. Biochemical and structural analysis of the enzymatic components of the CarPUL promoted the development of a detailed model of the κ/ι-carrageenan metabolic pathway deployed by pseudoalteromonads, thus furthering our understanding of how these microbes have adapted to a unique environmental niche.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Broad SARS-CoV-2 neutralization by monoclonal and bispecific antibodies derived from a Gamma-infected individual

The pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has remained a medical threat due to the evolution of multiple variants that acquire resistance to vaccines and prior infection. Therefore, it is imperative to discover monoclonal antibodies (mAbs) that neutralize a broad range of SARS-CoV-2 variants. A stabilized spike glycoprotein was used to enrich antigen-specific B cells from an individual with a primary Gamma variant infection. Five mAbs selected from those B cells showed considerable neutralizing potency against multiple variants, with COVA309-35 being the most potent against the autologous virus, as well as Omicron BA.1 and BA.2, and COVA309-22 having binding and neutralization activity against Omicron BA.4/5, BQ.1.1, and XBB.1. When combining the COVA309 mAbs as cocktails or bispecific antibodies, the breadth and potency were improved. In addition, the mechanism of cross-neutralization of the COVA309 mAbs was elucidated by structural analysis. Altogether these data indicate that a Gamma-infected individual can develop broadly neutralizing antibodies.

60 APPLIED LIFE SCIENCES↗