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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 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Development of a scalar-based geometric parameterization approach for the crystal structure landscape of dithienylethene-based crystalline solids

Dithienylethenes (DTEs) are a promising class of organic photoswitches that can be used to create crystalline solids with properties controlled by light. However, the ability of DTEs to adopt multiple conformations, only one of which is photoactive, complicates the rational design of these materials. Herein, the synthesis and structural characterization of 19 crystalline solids containing a single DTE molecule are described. A novel D – D analysis of the molecular geometries obtained from rotational potential energy surface calculations and the ensemble of experimental structures were used to construct a crystal landscape for DTE. Of the 19 crystal structures, 17 contained photoinactive DTE rotamers and only 2 were photoactive. These results highlight the challenges associated with the design of these materials. Overall, the D – D analysis described herein provides rapid, effective and intuitive means of linking the molecular structure to photoactivity that could be applied more broadly to afford a general strategy for producing photoactive diarylethene-based crystalline solids.

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

Mapping the structural–mechanical landscape of amorphous carbon with ReaxFF molecular dynamics

We use ReaxFF molecular dynamics (MD) to investigate the relationship between structural and mechanical properties in bulk and nanostructured amorphous carbon (a-C). The liquid-quench MD method is used to generate isotropic bulk samples with mass densities ranging from 0.96 to 3.29 g/cm3. Structural analysis identifies two types of structures with distinct short- and medium-range order: lower-density sp2-dominated a-C, which is characterized by a bimodal ring-size distribution, and higher-density sp3-dominated tetrahedral amorphous carbon (ta-C), exhibiting a unimodal ring-size distribution. Stress–strain MD simulations and analysis reveal how an atomistic structure impacts elastic properties and post-yield atomic rearrangements. All stretched structures demonstrate elastic isotropy and plasticity driven by a ring-size expansion mechanism reflected in changes in ring statistics. The plastic region is substantially larger in ta-C than in a-C due to the post-yield shift from sp3 to sp2 C dominant bonding. In both a-C and ta-C, ultimate failure occurs when a reactive crack, traversed by long sp chains, forms and propagates predominantly perpendicular to the direction of the applied strain. Oxygen infiltration into the fractured region significantly reduces stress resistance, primarily through the early rupture of long sp chains. MD simulations and analysis are extended to a-C slabs, a-C nanotubes, and partially a-C nanotubes. The latter nanostructure highlights the differences between the elastically isotropic a-C walls, which develop circumferential cracking, and the crystalline walls, which tear along crystallographic directions. These results provide a strong foundation for further computational characterization of a-C materials.

Dernov, A. (ORCID:0009000004220973)↗
DOE OSTI2024

Landscape fragmentation overturns classical metapopulation thinking

Habitat loss and isolation caused by landscape fragmentation represent a growing threat to global biodiversity. Existing theory suggests that the process will lead to a decline in metapopulation viability. However, since most metapopulation models are restricted to simple networks of discrete habitat patches, the effects of real landscape fragmentation, particularly in stochastic environments, are not well understood. To close this major gap in ecological theory, we developed a spatially explicit, individual-based model applicable to realistic landscape structures, bridging metapopulation ecology and landscape ecology. This model reproduced classical metapopulation dynamics under conventional model assumptions, but on fragmented landscapes, it uncovered general dynamics that are in stark contradiction to the prevailing views in the ecological and conservation literature. Notably, fragmentation can give rise to a series of dualities: a) positive and negative responses to environmental noise, b) relative slowdown and acceleration in density decline, and c) synchronization and desynchronization of local population dynamics. Furthermore, counter to common intuition, species that interact locally (“residents”) were often more resilient to fragmentation than long-ranging “migrants.” This set of findings signals a need to fundamentally reconsider our approach to ecosystem management in a noisy and fragmented world.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Unveiling X-ray absorption signatures of boron nitride via first-principles simulation and machine learning

Boron nitride (BN) allotropes hold great promise in many advanced applications ranging from optical and photonic devices to energy storage and battery systems to tribological components. The diverse functionalities of this material stem from BN’s highly tunable structural and electronic properties, which are governed by the versatile boron–nitrogen bonding configurations. Exploring the structural landscape of BN can unveil novel structures possessing unique properties suited for specific applications, therefore accelerating the design of next-generation advanced functional materials. In this work, we leverage boron K-edge X-ray absorption spectroscopy (XAS) as an effective probe for local structural features and chemical environments. A total of 210 BN crystal structures are generated via analogies to the extensive array of carbon allotropes, and XAS is simulated for each unique local motif within the resulting collection of structures. A mapping between structural features and spectral signatures was established by synergizing first-principle simulations with data-driven based post-analysis approaches. Specifically, we developed a neural network model that can satisfactorily predict spectra line shapes from local structural descriptors. Toward automatic spectroscopic interpretation of any new BN structures, supervised machine learning models, trained on this structure–spectrum dataset, can accurately infer local coordination environments from simulated XAS, highlighting the strength of this unique approach of combining high-fidelity first-principles simulation and machine-learning to accelerate target design of novel BN materials via rational understanding of local structure-spectrum correlations.

36 MATERIALS SCIENCE↗
DOE OSTI2026

RCSB protein data Bank: Next‐generation advanced search for exploration of experimental structures and computed structure models

Abstract The Protein Data Bank (PDB), established in 1971, is the primary global, open‐access archive for experimentally determined 3D macromolecular structures (proteins, RNA, DNA). The research‐focused RCSB.org web‐portal provides access to these data alongside more than one million machine‐learning‐predicted structure models, greatly expanding the available structural landscape. Rapid growth of both experimental and computational structures has increased the need for powerful yet accessible search tools that serve a broad and diverse scientific community. Herein, we describe a redesigned RCSB Protein Data Bank RCSB.org Advanced Search capability that supports intuitive discovery of 3D structures through a unified interface. This interface integrates annotation‐, sequence‐, and 3D structure‐based searches, embeds an interactive 3D viewer, and incorporates curated biological knowledge, such as catalytic site definitions from Mechanism and Catalytic Site Atlas and ligand‐guided structural motifs, for constructing geometry‐driven queries. A new Chemical Search tool allows definition of chemical queries via an integrated drawing tool or standard identifiers, seamlessly combining them with annotation filters. By allowing query definition directly within spatial and chemical contexts, these search interfaces reduce the need for detailed knowledge of residue numbering, chain identifiers, or external cheminformatics software. This capability enables efficient exploration of structures, chemical diversity, and structure–function relationships across all life domains. The redesigned interfaces can be accessed directly at rcsb.org/search/advanced for Advanced Search and rcsb.org/search/chemical for Chemical Search.

Rose, Yana [Research Collaboratory for Structural ↗
DOE OSTI2025

Understanding Differences in Water Adsorption Isotherms: Structural Variations, Force Fields, and Monte Carlo Simulation Approaches

Accurate prediction of water adsorption in micro- and mesoporous materials with hydrophobic pores is essential for the design and characterization of advanced adsorbent materials for separation and energy applications. Here, we assess the reproducibility and consistency of water adsorption isotherms in two microporous all-silica MFI zeolite structures (MFI-K and MFI-O) using two different zeolite force fields and three simulation approaches: grand canonical Monte Carlo (GCMC), Gibbs ensemble Monte Carlo (GEMC), and transition matrix Monte Carlo (TMMC). We demonstrate that consistent treatment of the bulk fluid phase in GCMC and TMMC simulations is critical for reconciling isotherms across methods, and we construct simulation-based equations of state for the TIP4P water model to enable rigorous fugacity-to-pressure conversions. Large shifts in the isotherms are observed for two zeolite force fields developed using different parametrization strategies, with the GCS force field representing implicitly a defect-containing all-silica zeolite, whereas the TraPPE-zeo force field accurately represents an essentially defect-free all-silica zeolite. While water in the van Koningsveld structure of MFI exhibits a first-order phase transition and condensation-like step for adsorption near room temperature, water in the Olson structure of MFI displays continuous adsorption, attributed to differences in the adsorption free energy landscapes. Structural analysis reveals that small geometric variations, particularly Si–O–Si bond angles near the strongest adsorption sites, lead to these substantial differences in adsorption behavior. Furthermore, our results highlight the sensitivity of simulated water adsorption isotherms in hydrophobic frameworks to seemingly small differences in the framework structures, force field parametrization, and simulation approaches.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Peripheral positions encode transport specificity in the small multidrug resistance exporters

In secondary active transporters, a relatively limited set of protein folds have evolved diverse solute transport functions. Because of the conformational changes inherent to transport, altering substrate specificity typically involves remodeling the entire structural landscape, limiting our understanding of how novel substrate specificities evolve. In the current work, we examine a structurally minimalist family of model transport proteins, the small multidrug resistance (SMR) transporters, to understand the molecular basis for the emergence of a novel substrate specificity. We engineer a selective SMR protein to promiscuously export quaternary ammonium antiseptics, similar to the activity of a clade of multidrug exporters in this family. Using combinatorial mutagenesis and deep sequencing, we identify the necessary and sufficient molecular determinants of this engineered activity. Using X-ray crystallography, solid-supported membrane electrophysiology, binding assays, and a proteoliposome-based quaternary ammonium antiseptic transport assay that we developed, we dissect the mechanistic contributions of these residues to substrate polyspecificity. We find that substrate preference changes not through modification of the residues that directly interact with the substrate but through mutations peripheral to the binding pocket. Our work provides molecular insight into substrate promiscuity among the SMRs and can be applied to understand multidrug export and the evolution of novel transport functions more generally.

Science & Technology - Other Topics↗
DOE OSTI2024

Diabatic Valence-Hole Concept

A global diabatization scheme, based on the “valence-hole” concept, has been previously applied to model webs of avoided crossings that exist in four electronic-state symmetry manifolds of C 2 ( 1 Π g , 3 Π g , 1 Σ u + , and 3 Σ u + ). Here, this model is extended to the electronically excited states of four more molecules: CN ( 2 Σ + ), N 2 ( 3 Π u ), SiC ( 3 Π), and Si 2 ( 3 Π g ). Many strangenesses in the spectroscopic observations (e.g., energy level structure, predissociation linewidths, and radiative lifetimes) for all four electronic state systems discussed here are accounted for by this unified model. The key concept of the model is valence-hole electron configurations: 3σ 2 4σ 1 1π 4 5σ 2 in CN ( 2 Σ + ), 2σ g 2 2σ u 1 1π u 4 3σ g 2 1π g 1 in N 2 ( 3 Π u ), 5σ 2 6σ 1 7σ 2 2π 3 in SiC ( 3 Π), and 4σ g 2 4σ u 1 5σ g 2 2π u 3 in Si 2 ( 3 Π g ), all of which have a triply occupied “valence-core” (i.e., 2σ g 2 2σ u 1 or the equivalent). These valence-hole configurations have a nominal bond order of three or higher and correlate with high-energy separated-atom limits with an np ← ns (n = 2, 3) promotion in one of the atomic constituents. On its way to dissociation, the strongly bound diabatic valence-hole state crosses multiple weakly bound or repulsive states, which belong to electron configurations with a completely filled valence-core. These curve crossings between diabatic potentials result in a network of many avoided crossings among multiple electronic states, analogous to the well-studied electronic structure landscape of ionic-covalent crossings in strongly ionic molecules. In conclusion, considering the unique role of valence-hole states in shaping the global electronic structure, the valence-hole concept should be added to our intuitive framework of chemical bonding.

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

Generative $β$-hairpin design using a residue-based physicochemical property landscape

De novo peptide design is a new frontier that has broad application potential in the biological and biomedical fields. Most existing models for de novo peptide design are largely based on sequence homology that can be restricted based on evolutionarily derived protein sequences and lack the physicochemical context essential in protein folding. Generative machine learning for de novo peptide design is a promising way to synthesize theoretical data that are based on, but unique from, the observable universe. In this study, we created and tested a custom peptide generative adversarial network intended to design peptide sequences that can fold into the -hairpin secondary structure. This deep neural network model is designed to establish a preliminary foundation of the generative approach based on physicochemical and conformational properties of 20 canonical amino acids, for example, hydrophobicity and residue volume, using extant structure-specific sequence data from the PDB. The beta generative adversarial network model robustly distinguishes secondary structures of hairpin from α helix and intrinsically disordered peptides with an accuracy of up to 96% and generates artificial -hairpin peptide sequences with minimum sequence identities around 31% and 50% when compared against the current NCBI PDB and nonredundant databases, respectively. These results highlight the potential of generative models specifically anchored by physicochemical and conformational property features of amino acids to expand the sequence-to-structure landscape of proteins beyond evolutionary limits.

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

Dimensional Control in Phase-Pure Coevaporated Quasi-2D Ruddlesden–Popper Structures

Fast, uncontrolled crystallization with several competing pathways makes solution-processing of phase-pure quasi-two-dimensional (quasi-2D) metal halide Ruddlesden–Popper thin films challenging. Typically, solution-processing results in the formation of different structural phases with varying dimensionality ranging from 2D, to quasi-2D, and 3D, introducing bandgap disorder and inhibiting charge transport. In this work, we eliminate interactions between precursor salts and solvents by using controlled thermal coevaporation to grow quasi-2D thin films that show high phase purity and narrow phase distribution. We study the structural landscape using synchrotron-based X-ray scattering and charge-carrier dynamics using ultrafast pump–probe spectroscopy. We then demonstrate a strategy to control the crystallographic phase of the film through phosphonic acid-based surface modification. We use density functional theory to study the interactions between propylphosphonic acid and the organic precursors and find that the interactions of loosely bound phosphonic acid molecules with evaporated precursors, followed by the migration of phosphonic acids through the deposited thin film, dictate the film structure between 2D and quasi-2D phases. These findings introduce new solvent-free methods for the fabrication of phase-pure quasi-2D Ruddlesden–Popper thin films and control phase selectivity across different dimensional (2D and quasi-2D) structures.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Search for Stable and Low-Energy Ce–Co–Cu Ternary Compounds Using Machine Learning

Cerium-based intermetallics have garnered significant research attention as potential new permanent magnets. In this study, we explore the compositional and structural landscape of Ce−Co−Cu ternary compounds using a machine learning (ML)- guided framework integrated with first-principles calculations. We employ a crystal graph convolutional neural network (CGCNN), which enables efficient screening for promising candidates, significantly accelerating the material discovery process. With this approach, we predict five stable compounds, Ce 3 Co 3 Cu, CeCoCu 2 , Ce 12 Co 7 Cu, Ce 11 Co 9 Cu, and Ce 10 Co 11 Cu 4 , with formation energies below the convex hull, along with hundreds of low-energy (possibly metastable) Ce−Co−Cu ternary compounds. Firstprinciples calculations reveal that several structures are both energetically and dynamically stable. Notably, two Co-rich low-energy compounds, Ce 4 Co 33 Cu and Ce 4 Co 31 Cu 3 , are predicted to have high magnetizations.

Chemical structure↗
DOE OSTI2025

A Panoramic View of MXenes via an Atomic Coordination‐Based Design Strategy

Two‐dimensional (2D) transition metal carbides and nitrides, known as MXenes, possess unique physical and chemical properties, enabling diverse applications in fields ranging from energy storage to communication, catalysis, sensing, healthcare, and beyond. Despite extensive research and notable advancements, a fundamental understanding of MXenes’ phase diversity and its connection to their hierarchical precursors, including the intermediate MAX phases and the ancestral bulk phases, remains limited. Here, in this study, it is hypothesized that the atomic coordination environments adopted by transition metal and nonmetallic atoms in their three‐dimensional (3D) bulk precursors may persist in 2D MXenes to govern their phase diversity. Using high‐throughput modeling based on first‐principles density functional theory, a wide range of MXene phases is unveiled and comprehensively evaluate their relative stabilities across a large chemical space. The key to the approach lies in considering various atomic coordination environments drawn from four types of ancestral bulk phases. Through this comprehensive structural library of MXenes, general guiding principles are uncovered, such as a close alignment between the phase stability of MXenes and that of their 3D precursors. These findings introduce a new design strategy in which the atomic coordination environments in bulk phases can serve as reliable predictors for accessing the diverse structural landscape of MXenes.

MXenes↗
DOE OSTI2025

Li 21 Ge 8 P 3 S 34 : New Lithium Superionic Conductor with Unprecedented Structural Type

Abstract Lithium superionic conductors are pivotal for enabling all‐solid‐state batteries, which aim to replace liquid electrolytes and enhance safety. Herein, we report the discovery of an unprecedented lithium superionic conductor, Li 21 Ge 8 P 3 S 34 , featuring a novel structural type and a new composition in the Li–Ge–P–S system. This material exhibits high lithium ionic conductivity of approximately 1.0 mS cm −1 at 303 K with a low activation energy of 0.20(1) eV. It's unique crystal structure was elucidated using three‐dimensional electron diffraction (3D ED) and further refined through combined powder X‐ray and neutron diffraction analyses. The structure consists of alternating two‐dimensional slabs: one of corner‐sharing GeS 4 tetrahedra and the other of isolated PS 4 tetrahedra, enabling efficient lithium‐ion transport through a tetrahedrally interconnected network of 1D, 2D, and 3D diffusion pathways. This distinctive structural motif provides a novel design strategy for next‐generation solid electrolytes, broadening the structural landscape of lithium superionic conductors. With further advancements in compositional tuning and interfacial engineering, Li 21 Ge 8 P 3 S 34 could contribute to the development of high‐performance all‐solid‐state batteries.

Chemistry↗
DOE OSTI2024

Crystallography Reveals Metal‐Triggered Restructuring of β‐Hairpins

Abstract Metal binding to β‐sheets occurs in many metalloproteins and is also implicated in the pathology of Alzheimer's disease. De novo designed metallo‐β‐sheets have been pursued as models and mimics of these proteins. However, no crystal structures of canonical β‐sheet metallopeptides have yet been obtained, in stark contrast to many examples for ɑ‐helical metallopeptides, leading to a poor understanding for their chemistry. To address this, we have engineered tryptophan zippers, stable 12‐residue β‐sheet peptides, to bind Cu(II) ions and obtained crystal structures through single crystal X‐ray diffraction (SC‐XRD). We find that metal binding triggers several unexpected supramolecular assemblies that demonstrate the range of higher‐order structures available to metallo‐β‐sheets. Overall, these findings underscore the importance of crystallography in elucidating the rich structural landscape of metallo‐β‐sheet peptides.

Thuc Dang, Viet↗
DOE OSTI2024

Removing Fluoride from Double Four-Membered Rings Yielding Defect-Free Zeolites under Mild Conditions Using Ozone

We have investigated ozone treatment of as-made LTA zeolites under mild temperature conditions (175 °C) using experiments and periodic DFT as a method of energy savings and engineering defects such as silanol nests in comparison with conventional calcination at 550 °C. We have studied ozone treatment on LTA samples synthesized with 1,2-dimethyl-3-(4-methylbenzyl) imidazolium (denoted as “BULKY”) as the primary organic structure-directing agent (OSDA) and with various amounts of tetramethylammonium (TMA) as a secondary OSDA. Ozone treatment of LTA-BULKY at 175 °C was found to give defect-free, pristine LTA materials as determined by 29 Si NMR, 13 C NMR, Raman spectra, and DFT to assign the spectra. This represents a significant and unexpected finding: that fluoride ions can be completely removed from double four-membered rings (D4Rs) under such mild conditions. Furthermore, ozone treatment of LTA-BULKY-TMA samples removed BULKY but left behind TMA/F, giving a new and more diverse structural landscape of Si environments in LTA. Ab initio MetaDynamics calculations provide pathways with relatively low barriers, explaining how fluoride ions can be removed from D4Rs, leaving behind defect-free LTA materials under mild conditions.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Cryo-EM structures reveal native GABA A receptor assemblies and pharmacology

Type A γ-aminobutyric acid receptors (GABA A Rs) are the principal inhibitory receptors in the brain and the target of a wide range of clinical agents, including anaesthetics, sedatives, hypnotics and antidepressants. However, our understanding of GABA A R pharmacology has been hindered by the vast number of pentameric assemblies that can be derived from 19 different subunits and the lack of structural knowledge of clinically relevant receptors. Here, we isolate native murine GABA A R assemblies containing the widely expressed α1 subunit and elucidate their structures in complex with drugs used to treat insomnia (zolpidem (ZOL) and flurazepam) and postpartum depression (the neurosteroid allopregnanolone (APG)). Using cryo-electron microscopy (cryo-EM) analysis and single-molecule photobleaching experiments, we uncover three major structural populations in the brain: the canonical α1β2γ2 receptor containing two α1 subunits, and two assemblies containing one α1 and either an α2 or α3 subunit, in which the single α1-containing receptors feature a more compact arrangement between the transmembrane and extracellular domains. Interestingly, APG is bound at the transmembrane α/β subunit interface, even when not added to the sample, revealing an important role for endogenous neurosteroids in modulating native GABA A Rs. Together with structurally engaged lipids, neurosteroids produce global conformational changes throughout the receptor that modify the ion channel pore and the binding sites for GABA and insomnia medications. Our data reveal the major α1-containing GABA A R assemblies, bound with endogenous neurosteroid, thus defining a structural landscape from which subtype-specific drugs can be developed.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Structure of an RNA G-quadruplex from the West Nile virus genome

Potential G-quadruplex sites have been identified in the genomes of DNA and RNA viruses and proposed as regulatory elements. The genus Orthoflavivirus contains arthropod-transmitted, positive-sense, single-stranded RNA viruses that cause significant human disease globally. Computational studies have identified multiple potential G-quadruplex sites that are conserved across members of this genus. Subsequent biophysical studies established that some G-quadruplexes predicted in Zika and tickborne encephalitis virus genomes can form and known quadruplex binders reduced viral yields from cells infected with these viruses. The susceptibility of RNA to degradation and the variability of loop regions have made structure determination challenging. Despite these difficulties, we report a high-resolution structure of the NS5-B quadruplex from the West Nile virus genome. Analysis reveals two stacked tetrads that are further stabilized by a stacked triad and transient noncanonical base pairing. This structure expands the landscape of solved RNA quadruplex structures and demonstrates the diversity and complexity of biological quadruplexes. We anticipate that the availability of this structure will assist in solving further viral RNA quadruplexes and provides a model for a conserved antiviral target in Orthoflavivirus genomes.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Sequence-structure-function characterization of the emerging tetracycline destructase family of antibiotic resistance enzymes

Tetracycline destructases (TDases) are flavin monooxygenases which can confer resistance to all generations of tetracycline antibiotics. The recent increase in the number and diversity of reported TDase sequences enables a deep investigation of the TDase sequence-structure-function landscape. Here, we evaluate the sequence determinants of TDase function through two complementary approaches: (1) constructing profile hidden Markov models to predict new TDases, and (2) using multiple sequence alignments to identify conserved positions important to protein function. Using the HMM-based approach we screened 50 high-scoring candidate sequences in Escherichia coli, leading to the discovery of 13 new TDases. The X-ray crystal structures of two new enzymes from Legionella species were determined, and the ability of anhydrotetracycline to inhibit their tetracycline-inactivating activity was confirmed. Using the MSA-based approach we identified 31 amino acid positions 100% conserved across all known TDase sequences. The roles of these positions were analyzed by alanine-scanning mutagenesis in two TDases, to study the impact on cell and in vitro activity, structure, and stability. These results expand the diversity of TDase sequences and provide valuable insights into the roles of important residues in TDases, and flavin monooxygenases more broadly.

60 APPLIED LIFE SCIENCES↗