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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 559 records · Page 31
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Cryo-EM structures of HIV-1 trimer bound to CD4-mimetics BNM-III-170 and M48U1 adopt a CD4-bound open conformation

Human immunodeficiency virus-1 (HIV-1), the causative agent of AIDS, impacts millions of people. Entry into target cells is mediated by the HIV-1 envelope (Env) glycoprotein interacting with host receptor CD4, which triggers conformational changes allowing binding to a coreceptor and subsequent membrane fusion. Small molecule or peptide CD4-mimetic drugs mimic CD4’s Phe43 interaction with Env by inserting into the conserved Phe43 pocket on Env subunit gp120. Here, we present single-particle cryo-EM structures of CD4-mimetics BNM-III-170 and M48U1 bound to a BG505 native-like Env trimer plus the CD4-induced antibody 17b at 3.7 Å and 3.9 Å resolution, respectively. CD4-mimetic-bound BG505 exhibits canonical CD4-induced conformational changes including trimer opening, formation of the 4-stranded gp120 bridging sheet, displacement of the V1V2 loop, and formation of a compact and elongated gp41 HR1C helical bundle. We conclude that CD4-induced structural changes on both gp120 and gp41 Env subunits are induced by binding to the gp120 Phe43 pocket.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Importance of interface open circuit potential on aqueous hydrogenolytic reduction of benzyl alcohol over Pd/C

Abstract The open circuit potential (OCP) established by the quasi-equilibrated electrode reaction of H 2 and H 3 O + (hydr.) , complicates catalytic reactions significantly. The hydrogenolysis rate of benzylic alcohol on Pd/C increases 2-3 orders of magnitude with the pH decreasing from 7 to 0.6. The reaction follows a pathway of protonated benzyl alcohol dehydration to a benzylic carbenium ion, followed by a hydride addition to form toluene. The dehydration of protonated benzyl alcohol is kinetic relevent, thus, being enhanced at lower pH. The OCP stabilizes all cationic species in the elementary steps. Particularly, the initial state (benzyl alcohol oxonium ion) is less stabilized than the dehydration transition state and the product (benzylic carbenium), thus, lowering the free energy barrier of the rate-determining step. In accordance, the rate increased with increasingly negative OCP. Beside OCP, an external negative electric potential in an electrocatlaytic system was also demonstrated to enhance the rate in the same way.

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

Open access repository-scale propagated nearest neighbor suspect spectral library for untargeted metabolomics

Despite the increasing availability of tandem mass spectrometry (MS/MS) community spectral libraries for untargeted metabolomics over the past decade, the majority of acquired MS/MS spectra remain uninterpreted. To further aid in interpreting unannotated spectra, we created a nearest neighbor suspect spectral library, consisting of 87,916 annotated MS/MS spectra derived from hundreds of millions of MS/MS spectra originating from published untargeted metabolomics experiments. Entries in this library, or “suspects,” were derived from unannotated spectra that could be linked in a molecular network to an annotated spectrum. Annotations were propagated to unknowns based on structural relationships to reference molecules using MS/MS-based spectrum alignment. We demonstrate the broad relevance of the nearest neighbor suspect spectral library through representative examples of propagation-based annotation of acylcarnitines, bacterial and plant natural products, and drug metabolism. Our results also highlight how the library can help to better understand an Alzheimer’s brain phenotype. The nearest neighbor suspect spectral library is openly available for download or for data analysis through the GNPS platform to help investigators hypothesize candidate structures for unknown MS/MS spectra in untargeted metabolomics data.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Active light-controlled frontal ring-opening metathesis polymerization

Frontal ring-opening metathesis polymerization (FROMP) is a promising energy-efficient approach to fabricate polymeric materials. Recent advances have demonstrated FROMP for diverse applications, including additive manufacturing, composites, and foams. However, the characteristic properties of the front are currently controlled primarily by varying the resin composition or the environmental conditions. In this work we present an approach to control FROMP of dicyclopentadiene (DCPD) using photochemical methods. A photobase generator is used to inhibit FROMP of DCPD with UV light while a photosensitizer and co-initiator are used to accelerate FROMP with blue light, enabling orthogonal active photocontrol of front velocity. In addition, photoinhibition-enabled lithographic patterning of frontal polymerizations is demonstrated. Frontal polymerizations are spatially controlled, redirected, and even split into diverging fronts. This work establishes a foundation for advanced control of frontal polymerizations, enabling innovation in traditional and additive manufacturing, as well as emerging processes like morphogenic manufacturing.

Polymer synthesis↗
DOE OSTI2026

Valence-free open nanoparticle superlattices

A cornerstone of advanced materials design is establishing a framework for assembling nanoparticle superstructures with tailored symmetries. A longstanding challenge has been assembling diamond-like superstructures for photonic devices. Traditionally, such open superstructures require functionalized nanoparticles with directional or anisotropic interactions, reminiscent of valence bonding in a diamond. Here, we present a robust strategy for assembling valence-free nanoparticles into a broad array of cubic superstructures. By grafting nanoparticles with oppositely charged, end-functionalized water-soluble polymers of adjustable molecular weight, we gain control over electrostatic interactions and conformational constraints. This unified approach yields lattices analogous to rock salt, CsCl, zinc-blende, diamond, and the rare simple cubic phase, with tunable lattice constants. Theoretical models and simulations elucidate the underlying interactions, providing a framework for engineering valence-free nanoparticle superlattices.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Materials Graph Library (MatGL), an open-source graph deep learning library for materials science and chemistry

Graph deep learning models, which incorporate a natural inductive bias for atomic structures, are of immense interest in materials science and chemistry. Here, we introduce the Materials Graph Library (MatGL), an open-source graph deep learning library for materials science and chemistry. Built on top of the popular Deep Graph Library (DGL) and Python Materials Genomics (Pymatgen) packages, MatGL is designed to be an extensible “batteries-included” library for developing advanced model architectures for materials property predictions and interatomic potentials. At present, MatGL has efficient implementations for both invariant and equivariant graph deep learning models, including the Materials 3-body Graph Network (M3GNet), MatErials Graph Network (MEGNet), Crystal Hamiltonian Graph Network (CHGNet), TensorNet and SO3Net architectures. MatGL also provides several pre-trained foundation potentials (FPs) with coverage of the entire periodic table, and property prediction models for out-of-box usage, benchmarking and fine-tuning. Finally, MatGL integrates with PyTorch Lightning to enable efficient model training.

chemistry↗
DOE OSTI2023

Tetrafluorenofulvalene as a sterically frustrated open-shell alkene

Electronic and steric effects are known to greatly influence the structure, characteristics and reactivity of organic compounds. A typical π bond is weakened by oxidation (corresponding to the removal of electrons from bonding orbitals), by reduction (through addition of electrons to antibonding orbitals) and by unpairing of the bonding electrons, such as in the triplet state. Here we describe tetrafluorenofulvalene (TFF), a twisted, open-shell alkene for which these general rules do not hold. Through the synthesis, experimental characterization and computational analysis of its charged species spanning seven redox states, the central alkene bond in TFF is shown to become substantially stronger in the tri- and tetraanion, generated by chemical reduction. Furthermore, although its triplet state contains a weaker alkene bond than the singlet, in the quintet state its bond order increases substantially, yielding a flatter structure. This behaviour originates from the doubly bifurcated topology of the underlying spin system and can be rationalized by the balancing effects of benzenoid aromaticity and spin pairing.

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

4f-orbital covalency enables a single-crystal-to-single-crystal ring-opening isomerization in a CeIV–cyclopropenyl complex

Metal–ligand bonding interactions for f-element compounds are typically highly polarized with only minor covalent character. Whereas the 5d/6d orbitals are known to be chemically accessible for dative bonding, recent quantum chemical and spectroscopic analyses have indicated appreciable 4f/5f-orbital involvement in certain metal–ligand bonds. However, 4f-orbital covalency has not been compellingly linked to distinctive modes of chemical reactivity via rigorous comparative study and mechanistic investigation. Here a series of MIV–cyclopropenyl complexes (M = Ti, Zr, Ce, Hf, Th) are described, wherein the cerium congener exhibits a 4f-covalent Ce=Cα interaction, causing a ring-opening isomerization reaction through a single-crystal-to-single-crystal transformation. The results provide evidence for 4f-orbital covalency by demonstrating its expression in the reactivity of an f-element complex within an isostructural series of tetravalent d- and f-block metal complexes. They also provide new directions for the study of orbital covalency effects of molecular compounds in solid-state chemical transformations.

Vincenzini, Brett D↗
DOE OSTI2024

Kainate receptor channel opening and gating mechanism

Kainate receptors, a subclass of ionotropic glutamate receptors, are tetrameric ligand-gated ion channels that mediate excitatory neurotransmission. Kainate receptors modulate neuronal circuits and synaptic plasticity during the development and function of the central nervous system and are implicated in various neurological and psychiatric diseases, including epilepsy, depression, schizophrenia, anxiety and autism. Although structures of kainate receptor domains and subunit assemblies are available, the mechanism of kainate receptor gating remains poorly understood. Here we present cryo-electron microscopy structures of the kainate receptor GluK2 in the presence of the agonist glutamate and the positive allosteric modulators lectin concanavalin A and BPAM344. Concanavalin A and BPAM344 inhibit kainate receptor desensitization and prolong activation by acting as a spacer between the amino-terminal and ligand-binding domains and a stabilizer of the ligand-binding domain dimer interface, respectively. Channel opening involves the kinking of all four pore-forming M3 helices. Our structures reveal the molecular basis of kainate receptor gating, which could guide the development of drugs for treatment of neurological disorders.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Unravelling the diversity of magnetotactic bacteria through analysis of open genomic databases

Magnetotactic bacteria (MTB) are prokaryotes that possess genes for the synthesis of membrane-bounded crystals of magnetite or greigite, called magnetosomes. Despite over half a century of studying MTB, only about 60 genomes have been sequenced. Most belong to Proteobacteria, with a minority affiliated with the Nitrospirae, Omnitrophica, Planctomycetes, and Latescibacteria. Due to the scanty information available regarding MTB phylogenetic diversity, little is known about their ecology, evolution and about the magnetosome biomineralization process. This study presents a large-scale search of magnetosome biomineralization genes and reveals 38 new MTB genomes. Several of these genomes were detected in the phyla Elusimicrobia, Candidatus Hydrogenedentes, and Nitrospinae, where magnetotactic representatives have not previously been reported. Analysis of the obtained putative magnetosome biomineralization genes revealed a monophyletic origin capable of putative greigite magnetosome synthesis. The ecological distributions of the reconstructed MTB genomes were also analyzed and several patterns were identified. These data suggest that open databases are an excellent source for obtaining new information of interest.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

An open source knowledge graph ecosystem for the life sciences

Translational research requires data at multiple scales of biological organization. Advancements in sequencing and multi-omics technologies have increased the availability of these data, but researchers face significant integration challenges. Knowledge graphs (KGs) are used to model complex phenomena, and methods exist to construct them automatically. However, tackling complex biomedical integration problems requires flexibility in the way knowledge is modeled. Moreover, existing KG construction methods provide robust tooling at the cost of fixed or limited choices among knowledge representation models. PheKnowLator (Phenotype Knowledge Translator) is a semantic ecosystem for automating the FAIR (Findable, Accessible, Interoperable, and Reusable) construction of ontologically grounded KGs with fully customizable knowledge representation. The ecosystem includes KG construction resources (e.g., data preparation APIs), analysis tools (e.g., SPARQL endpoint resources and abstraction algorithms), and benchmarks (e.g., prebuilt KGs). We evaluated the ecosystem by systematically comparing it to existing open-source KG construction methods and by analyzing its computational performance when used to construct 12 different large-scale KGs. With flexible knowledge representation, PheKnowLator enables fully customizable KGs without compromising performance or usability.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗
DOE OSTI2025

Opening doors to physical sample tracking and attribution in Earth and environmental sciences

Physical samples and their associated data and metadata underpin scientific discoveries across disciplines and can enable new science when appropriately archived. However, there are significant gaps in current practices and infrastructure that prevent accurate provenance tracking, reproducibility, and attribution. For most samples, descriptive metadata are often sparse, inaccessible, or absent. Samples and associated data and metadata may also be scattered across numerous physical collections, data repositories, laboratories, data files, and papers with no clear linkage or provenance tracking as new information is generated over time. The Earth Science Information Partners (ESIP) Physical Samples Curation Cluster has therefore developed guidance for scientific authors on ‘Publishing Open Research Using Physical Samples.’ This involved synthesizing existing practices, gathering community feedback, and assessing real-world examples. We identified improvements needed to enable authors to efficiently cite and link Earth science samples and related data, and track their use. Our goal is to help improve discoverability, interoperability, and reuse of physical samples, and associated data and metadata. Though primarily focused on the needs of Earth and environmental sciences, these guidelines are broadly applicable.

58 GEOSCIENCES↗
DOE OSTI2021

Complex of human Melanotransferrin and SC57.32 Fab fragment reveals novel interdomain arrangement with ferric N-lobe and open C-lobe

Melanotransferrin (MTf) is an iron-binding member of the transferrin superfamily that can be membrane-anchored or secreted in serum. On cells, it can mediate transferrin-independent iron uptake and promote proliferation. In serum, it is a transcytotic iron transporter across the blood–brain barrier. MTf has been exploited as a drug delivery carrier to the brain and as an antibody-drug conjugate (ADC) target due to its oncogenic role in melanoma and its elevated expression in triple-negative breast cancer (TNBC). For treatment of TNBC, an MTf-targeting ADC completed a phase I clinical trial (NCT03316794). The structure of its murine, unconjugated Fab fragment (SC57.32) is revealed here in complex with MTf. The MTf N-lobe is in an active and iron-bound, closed conformation while the C-lobe is in an open conformation incompatible with iron binding. This combination of active and inactive domains displays a novel inter-domain arrangement in which the C2 subdomain angles away from the N-lobe. The C2 subdomain also contains the SC57.32 glyco-epitope, which comprises ten protein residues and two N-acetylglucosamines. Our report reveals novel features of MTf and provides a point of reference for MTf-targeting, structure-guided drug design.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

An open-source data storage and visualization platform for collaborative qubit control

Developing collaborative research platforms for quantum bit control is crucial for driving innovation in the field, as they enable the exchange of ideas, data, and implementation to achieve more impactful outcomes. Furthermore, considering the high costs associated with quantum experimental setups, collaborative environments are vital for maximizing resource utilization efficiently. However, the lack of dedicated data management platforms presents a significant obstacle to progress, highlighting the necessity for essential assistive tools tailored for this purpose. Current qubit control systems are unable to handle complicated management of extensive calibration data and do not support effectively visualizing intricate quantum experiment outcomes. In this paper, we introduce Qubit Control Storage and Visualization ( QubiCSV ), a platform specifically designed to meet the demands of quantum computing research, focusing on the storage and analysis of calibration and characterization data in qubit control systems. As an open-source tool, QubiCSV facilitates efficient data management of quantum computing, providing data versioning capabilities for data storage and allowing researchers and programmers to interact with qubits in real time. The insightful visualization are developed to interpret complex quantum experiments and optimize qubit performance. QubiCSV not only streamlines the handling of qubit control system data but also improves the user experience with intuitive visualization features, making it a valuable asset for researchers in the quantum computing domain.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

Structure of an anti-PEG antibody reveals an open ring that captures highly flexible PEG polymers

Polyethylene glycol (PEG) is a polymer routinely used to modify biologics and nanoparticles to prolong blood circulation and reduce immunogenicity of the underlying therapeutic. However, several PEGylated therapeutics induce the development of anti-PEG antibodies (APA), leading to reduced efficacy and increased adverse events. Given the highly flexible structure of PEG, how APA specifically bind PEG remains poorly understood. Here, we report a crystal structure illustrating the structural properties and conformation of the APA 6-3 Fab bound to the backbone of PEG. The structure reveals an open ring-like sub-structure in the Fab paratope, whereby PEG backbone is captured and then stabilized via Van der Waals interactions along the interior and exterior of the ring paratope surface. Our finding illustrates a strategy by which antibodies can bind highly flexible repeated structures that lack fixed conformations, such as polymers. This also substantially advances our understanding of the humoral immune response generated against PEG.

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

Open questions on the reactivity of Criegee intermediates

Criegee intermediates are reactive intermediates formed in Earth’s atmosphere through ozonolysis of alkenes. Here the authors outline the fundamental chemistry that influences their highly conformer- and substituent-dependent unimolecular and bimolecular reactivity, and discuss open questions of fundamental and atmospheric interest.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗