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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 73 records · Page 4
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

BGC Atlas: a web resource for exploring the global chemical diversity encoded in bacterial genomes

Secondary metabolites are compounds not essential for an organism’s development, but provide significant ecological and physiological benefits. These compounds have applications in medicine, biotechnology and agriculture. Their production is encoded in biosynthetic gene clusters (BGCs), groups of genes collectively directing their biosynthesis. The advent of metagenomics has allowed researchers to study BGCs directly from environmental samples, identifying numerous previously unknown BGCs encoding unprecedented chemistry. Here, we present the BGC Atlas (https://bgc-atlas.cs.uni-tuebingen.de), a web resource that facilitates the exploration and analysis of BGC diversity in metagenomes. The BGC Atlas identifies and clusters BGCs from publicly available datasets, offering a centralized database and a web interface for metadata-aware exploration of BGCs and gene cluster families (GCFs). We analyzed over 35 000 datasets from MGnify, identifying nearly 1.8 million BGCs, which were clustered into GCFs. The analysis showed that ribosomally synthesized and post-translationally modified peptides are the most abundant compound class, with most GCFs exhibiting high environmental specificity. We believe that our tool will enable researchers to easily explore and analyze the BGC diversity in environmental samples, significantly enhancing our understanding of bacterial secondary metabolites, and promote the identification of ecological and evolutionary factors shaping the biosynthetic potential of microbial communities.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Predicting the Pseudocapacitive Windows for MXene Electrodes with Voltage-Dependent Cluster Expansion Models

MXene transition-metal carbides and nitrides are of growing interest for energy storage applications. These compounds are especially promising for use as pseudocapacitive electrodes due to their ability to convert energy electrochemically at fast rates. Using voltage-dependent cluster expansion models, we predict the charge storage performance of MXene pseudocapacitors for a range of electrode compositions. M 3 C 2 O 2 electrodes based on group-VI transition metals have up to 80% larger areal energy densities than prototypical titanium-based (e.g., Ti 3 C 2 O 2 ) MXene electrodes. We attribute this high pseudocapacitance to the Faradaic voltage windows of group-VI MXene electrodes, which are predicted to be 1.2 to 1.8 times larger than those of titanium-based MXenes. The size of the pseudocapacitive voltage window increases with the range of oxidation states that are accessible to the MXene transition metals. Here, by similar mechanisms, the presence of multiple ions in the solvent (Li + and H + ) leads to sharp changes in the transition-metal oxidation states and can significantly increase the charge capacity of MXene pseudocapacitors.

36 MATERIALS SCIENCE↗
DOE OSTI2023

X-ray absorption spectroscopy study of Mn reference compounds for Mn speciation in terrestrial surface environments

Abstract X-ray absorption spectroscopy (XAS) offers great potential to identify and quantify Mn species in surface environments by means of linear combination fit (LCF), fingerprint, and shell-fit analyses of bulk Mn XAS spectra. However, these approaches are complicated by the lack of a comprehensive and accessible spectrum library. Additionally, molecular-level information on Mn coordination in some potentially important Mn species occurring in soils and sediments is missing. Therefore, we investigated a suite of 32 natural and synthetic Mn reference compounds, including Mn oxide, oxyhydroxide, carbonate, phosphate, and silicate minerals, as well as organic and adsorbed Mn species, by Mn K-edge X-ray absorption near edge structure (XANES) and extended X-ray absorption fine structure (EXAFS) spectroscopy. The ability of XAS to infer the average oxidation state (AOS) of Mn was assessed by comparing XANES-derived AOS with the AOS obtained from redox titrations. All reference compounds were studied for their local (<5 Å) Mn coordination environment using EXAFS shell-fit analysis. Statistical analyses were employed to clarify how well and to what extent individual Mn species (groups) can be distinguished by XAS based on spectral uniqueness. Our results show that LCF analysis of normalized XANES spectra can reliably quantify the Mn AOS within ~0.1 v.u. in the range +2 to +4. These spectra are diagnostic for most Mn species investigated, but unsuitable to identify and quantify members of the manganate and Mn(III)-oxyhydroxide groups. First-derivative XANES fingerprinting allows the unique identification of pyrolusite, ramsdellite, and potentially lithiophorite within the manganate group. However, XANES spectra of individual Mn compounds can vary significantly depending on chemical composition and/or crystallinity, which limits the accuracy of XANES-based speciation analyses. In contrast, EXAFS spectra provide a much better discriminatory power to identify and quantify Mn species. Principal component and cluster analyses of k2-weighted EXAFS spectra of Mn reference compounds implied that EXAFS LCF analysis of environmental samples can identify and quantify at least the following primary Mn species groups: (1) Phyllo- and tectomanganates with large tunnel sizes (2 × 2 and larger; hollandite sensu stricto, romanèchite, todorokite); (2) tectomanganates with small tunnel sizes (2 × 2 and smaller; cryptomelane, pyrolusite, ramsdellite); (3) Mn(III)-dominated species (nesosilicates, oxyhydroxides, organic compounds, spinels); (4) Mn(II) species (carbonate, phosphate, and phyllosilicate minerals, adsorbed and organic species); and (5) manganosite. All Mn compounds, except for members of the manganate group (excluding pyrolusite) and adsorbed Mn(II) species, exhibit unique EXAFS spectra that would allow their identification and quantification in mixtures. Therefore, our results highlight the potential of Mn K-edge EXAFS spectroscopy to assess bulk Mn speciation in soils and sediments. A complete XAS-based speciation analysis of bulk Mn in environmental samples should preferably include the determination of Mn valences following the “Combo” method of Manceau et al. (2012), EXAFS LCF analyses based on principal component and target transformation results, as well as EXAFS shell-fit analyses for the validation of LCF results. For this purpose, all 32 XAS reference spectra are provided in the Online Materials1 for further use by the scientific community.

Geochemistry & Geophysics↗
DOE OSTI2023

AdenPredictor: accurate prediction of the adenylation domain specificity of nonribosomal peptide biosynthetic gene clusters in microbial genomes

Microbial natural products represent a major source of bioactive compounds for drug discovery. Among these molecules, nonribosomal peptides (NRPs) represent a diverse class that include antibiotics, immunosuppressants, anticancer agents, toxins, siderophores, pigments, and cytostatics. The discovery of novel NRPs remains a laborious process because many NRPs consist of nonstandard amino acids that are assembled by nonribosomal peptide synthetases (NRPSs). Adenylation domains (A-domains) in NRPSs are responsible for selection and activation of monomers appearing in NRPs. During the past decade, several support vector machine-based algorithms have been developed for predicting the specificity of the monomers present in NRPs. These algorithms utilize physiochemical features of the amino acids present in the A-domains of NRPSs. In this article, we benchmarked the performance of various machine learning algorithms and features for predicting specificities of NRPSs and we showed that the extra trees model paired with one-hot encoding features outperforms the existing approaches. Moreover, we show that unsupervised clustering of 453560 A-domains reveals many clusters that correspond to potentially novel amino acids. While it is challenging to predict the chemical structure of these amino acids, we developed novel techniques to predict their various properties, including polarity, hydrophobicity, charge, and presence of aromatic rings, carboxyl, and hydroxyl groups.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Heterologous Expression of Cryptomaldamide in a Cyanobacterial Host

Filamentous marine cyanobacteria make a variety of bioactive molecules that are produced by polyketide synthases, nonribosomal peptide synthetases, and hybrid pathways that are encoded by large biosynthetic gene clusters. These cyanobacterial natural products represent potential drug leads; however, thorough pharmacological investigations have been impeded by the limited quantity of compound that is typically available from the native organisms. Additionally, investigations of the biosynthetic gene clusters and enzymatic pathways have been difficult due to the inability to conduct genetic manipulations in the native producers. Here we report a set of genetic tools for the heterologous expression of biosynthetic gene clusters in the cyanobacteria Synechococcus elongatus PCC 7942 and Anabaena (Nostoc) PCC 7120. To facilitate the transfer of gene clusters in both strains, we engineered a strain of Anabaena that contains S. elongatus homologous sequences for chromosomal recombination at a neutral site and devised a CRISPR-based strategy to efficiently obtain segregated double recombinant clones of Anabaena. These genetic tools were used to express the large 28.7 kb cryptomaldamide biosynthetic gene cluster from the marine cyanobacterium Moorena (Moorea) producens JHB in both model strains. S. elongatus did not produce cryptomaldamide; however, high-titer production of cryptomaldamide was obtained in Anabaena. Furthermore, the methods developed in this study will facilitate the heterologous expression of biosynthetic gene clusters isolated from marine cyanobacteria and complex metagenomic samples.

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

Cross-kingdom expression of synthetic genetic elements promotes discovery of metabolites in the human microbiome

Small molecules encoded by biosynthetic pathways mediate cross-species interactions and harbor untapped potential, which has provided valuable compounds for medicine and biotechnology. Since studying biosynthetic gene clusters in their native context is often difficult, alternative efforts rely on heterologous expression, which is limited by host-specific metabolic capacity and regulation. Here, in this work, we describe a computational-experimental technology to redesign genes and their regulatory regions with hybrid elements for cross-species expression in Gram-negative and -positive bacteria and eukaryotes, decoupling biosynthetic capacity from host-range constraints to activate silenced pathways. These synthetic genetic elements enabled the discovery of a class of microbiome-derived nucleotide metabolites—tyrocitabines—from Lactobacillus iners. Tyrocitabines feature a remarkable orthoester-phosphate, inhibit translational activity, and invoke unexpected biosynthetic machinery, including a class of “Amadori synthases” and “abortive” tRNA synthetases. Our approach establishes a general strategy for the redesign, expression, mobilization, and characterization of genetic elements in diverse organisms and communities.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Venturing Past Uranium: Synthesis of a Np(IV) Polyoxomolybdate–Alkoxide Sandwich Complex

The synthesis of a Np(IV) polyoxomolybdate– alkoxide sandwich complex, (TBA) 2 [Np{Mo 5 O 13 (OMe) 4 NO} 2 ] (TBA = tetrabutylammonium), is reported. This compound represents a rare example of a neptunium polyoxometalate cluster isolated outside of water, allowing for characterization of its electrochemical properties in nonaqueous solvents. Complexation of An(IV) cations fine-tunes the redox properties of the cluster, with the observed four reversible reductive events varying slightly both in potential and peak separation depending on the actinide present. The new Np(IV) complex also shows an irreversible event assigned to oxidation of Np(IV) to Np(V). New methodology for facile 17 O enrichment of (TBA) 2 [Mo 5 O 13 (OMe) 4 NO][Na(MeOH)] is presented, which provides a simple pathway to 17 O enriched analogues of the sandwich complexes discussed (Zr(IV), Hf(IV), Th(IV), U(IV), U(V), Np(IV)). 17 O NMR spectroscopy subsequently provides insights into both the nature of metal–oxygen bonding, as well as the influence of unpaired f-electrons on the local environment of the oxygen nuclei.

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

Actinomycetota isolated from the sponge Hymeniacidon perlevis as a source of novel compounds with pharmacological applications: diversity, bioactivity screening, and metabolomic analysis

Abstract Aims To combat health conditions, such as multi-resistant bacterial infections, cancer, and metabolic diseases, new drugs need to be urgently found and, in this respect, marine Actinomycetota have a high potential to produce secondary metabolites with pharmacological importance. We aimed to study the cultivable Actinomycetota community associated with a marine sponge from the Portuguese coast, Hymeniacidon perlevis, and investigate the potential of the retrieved isolates to produce compounds with antimicrobial, anticancer and anti-obesity properties. Methods and results The analysis of the 16S rRNA gene revealed 79 Actinomycetota isolates affiliated with 12 genera—Brachybacterium, Dietzia, Glutamicibacter, Gordonia, Micrococcus, Micromonospora, Nocardia, Nocardiopsis, Paenoartrhobacter, Rhodococcus, Streptomyces, and Tsukamurella, most of which affiliated with the genus Streptomyces. The screening of antimicrobial activity revealed 13 strains, all belonging to the Streptomyces genus, capable of inhibiting the growth of Candida albicans, Bacillus subtilis, or Staphylococcus aureus. Forty-three extracts exhibited cytotoxic activity against at least one tested cell line (HepG2, HCT-116, and hCMEC-D3). Three extracts that were active against the two cancer cell lines tested, did not reduce the viability of the non-cancer endothelial cell line, hCMEC-D3. One Gordonia strain exhibited anti-obesity activity, revealed by its ability to reduce the neutral lipids in zebrafish larvae. Mass spectrometry-based dereplication analysis of active extracts identified several compounds associated with known Actinomycetota natural products. Nonetheless, five clusters contained metabolites that did not match any annotated natural products, suggesting they may represent new bioactive molecules. Conclusions This work contributed to increase the knowledge on the diversity and bioactive potential of Actinomycetota associated with H. perlevis.

Fonseca, Ana C.↗
DOE OSTI2020

Materials Data on La2CdSb3 by Materials Project

(LaSb)2CdSb crystallizes in the tetragonal P4/mmm space group. The structure is zero-dimensional and consists of one cadmium compounds molecule, one stibium metallicum molecule, and two LaSb clusters. In each LaSb cluster, La3+ is bonded in a single-bond geometry to one Sb+2.67- atom. The La–Sb bond length is 2.73 Å. Sb+2.67- is bonded in a single-bond geometry to one La3+ atom.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Characterizing Polyoxovanadate‐Alkoxide Clusters Using Vanadium K‐Edge X‐Ray Absorption Spectroscopy

Abstract A number of technologies would benefit from developing inorganic compounds and materials with specific electronic and magnetic exchange properties. Unfortunately, designing compounds with these properties is difficult because metal⋅⋅⋅metal coupling schemes are hard to predict and control. Fully characterizing communication between metals in existing compounds that exhibit interesting properties could provide valuable insight and advance those predictive capabilities. One such class of molecules are the series of Lindqvist iron‐functionalized and hexavanadium polyoxovanadate‐alkoxide clusters, which we characterized here using V K‐edge X‐ray absorption spectroscopy. Substantial changes in the pre‐edge peak intensities were observed that tracked with the V 3 d ‐electron count. The data also suggested substantial delocalization between the vanadium cations. Meanwhile, the Fe III cations were electronically isolated from the polyoxovanadate core.

Meyer, Rachel L.↗
DOE OSTI2026

A High-Fidelity Molecular Model of the Cu(111) Repeating Unit

Dynamic processes at surfaces are central to heterogeneous catalysis, but their atomistic mechanism(s) can prove difficult to elucidate due to variations in material structure and the corresponding impact on reactivity. Moreover, disparities between reaction conditions and those employed for spectroscopic characterization at surfaces can inhibit detailed understanding of catalysis-relevant chemistries. Herein, we substantiate the so-called “cluster-surface” analogy by leveraging a low-valent tricopper architecture ( 1 ) as a model system for small molecule activation at Cu(111). Two reaction classes are explored: the adsorption of carbon monoxide (CO) and the dissociative adsorption of dihydrogen (H 2 ). These processes serve as an ideal testbed to compare the reactivity of a molecular cluster ( 1 ) to that of a heterogeneous surface, as both reactions have empirical data from measurements performed on crystalline Cu(111). Cluster 1 reversibly binds CO. Variable temperature NMR analysis with 13 CO reveals a favorable enthalpy but large negative entropy (−5.1 kcal × mol –1 and −22.9 cal × mol –1 × K –1 , respectively) for CO binding, affording a process that is marginally endergonic at room temperature (ΔG ads (298.15 K) = 1.7 ± 0.5 kcal × mol –1 ). Similarly, analogous to a Cu(111) surface, 1 is shown to oxidatively add (chemisorb) H 2 . Kinetic parameters were determined for this process and the activation enthalpy (8.4 ± 0.5 kcal × mol –1 ) closely mirrors that established for H 2 binding at the Cu(111) facet (6.0 to 12.4 kcal × mol –1 ). Together, these results showcase that a trinuclear cluster can reproduce the small molecule binding and activation energetics of a bulk crystalline surface, setting the stage for studying less-defined surface processes in an atomically precise molecular setting.

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

Global characterization of biosynthetic gene clusters in non-model eukaryotes using domain architectures

Abstract The majority of pharmaceuticals are derived from natural products, bioactive compounds naturally synthesized by organisms to provide evolutionary advantages. Although the rich evolutionary history of eukaryotic algal species implicates a high potential for natural product-based drug discovery, it remains largely untouched. This study investigates 2762 putative biosynthetic gene clusters (BGCs) from 212 eukaryotic algal genomes. To analyze a vast set of structurally diverse BGCs, we employed comparative analysis based on the vectorization of biosynthetic domains, referred to as biosynthetic domain architecture (BDA). By characterizing core biosynthetic machineries through BDA, we identified key BDAs of modular BGCs in diverse eukaryotes and introduced 16 candidate modular BGCs with similar BDAs to previously validated BGCs. This study provides a global characterization of eukaryotic algal BGCs, offering an alternative to laborious manual curation for BGC prioritization.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Family of Robust and Strongly Luminescent CuI-Based Hybrid Networks Made of Ionic and Dative Bonds

The CuI-derived inorganic–organic hybrid compounds are considered as promising phosphors for the lighting industry. Herein, exploiting N-monoalkylated hexaminium salts, [R-HMTA]X (R = Me, Et, Pr, and propargyl; X = Cl and I), as multibridging ligands, we have designed and synthesized a unique class of one-dimensional and two-dimensional hybrid CuI-materials. The reactions of these salts with CuI give rise to All-in-One (AIO) type compounds combining ionic and dative bonds between inorganic and organic components. The latter is formed by structurally unique inorganic [Cu x I y ] (y–x)– clusters, chains, or sheets interconnected through [R-HMTA] + cations via multiple Cu–N bonds. The so-designed compounds at ambient temperature exhibit tunable luminescence spanning from deep blue to red color (λ em = 430–625 nm) with microsecond lifetimes and the quantum efficiency of up to 78%. Remarkably, the AIO materials feature nontrivial excitation- (ED) and temperature-dependent (TD) luminescence, allowing their emission color to be finely adjusted from deep blue to red through changing the excitation wavelength and/or temperature. Based on the TD emission spectroscopy and theoretical calculations, a possible mechanism of the luminescence has been proposed. In conclusion, the very interesting luminescence characteristics coupled with good thermal and photostability render these AIO hybrid materials possible candidates for applications in energy-efficient lighting devices.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Prediction of Self-Diffusion in Binary Fluid Mixtures Using Artificial Neural Networks

Artificial neural networks (ANNs) were developed to accurately predict the self-diffusion constants for individual components in binary fluid mixtures. The ANNs were tested on an experimental database of 4328 self-diffusion constants from 131 mixtures containing 75 unique compounds. The presence of strong hydrogen bonding molecules may lead to clustering or dimerization resulting in non-linear diffusive behavior. To address this, self- and binary association energies were calculated for each molecule and mixture to provide information on intermolecular interaction strength and were used as input features to the ANN. An accurate, generalized ANN model was developed with an overall average absolute deviation of 4.1%. Forward input feature selection reveals the importance of critical properties and self-association energies along with other fluid properties. Additional ANNs were developed with subsets of the full input feature set to further investigate the impact of various properties on model performance. The results from two specific mixtures are discussed in additional detail: one providing an example of strong hydrogen bonding and the other an example of extreme pressure changes, with the ANN models predicting self-diffusion well in both cases.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

Ultrafast optical melting of trimer superstructure in layered 1T′-TaTe2

Abstract Quasi-two-dimensional transition-metal dichalcogenides are a key platform for exploring emergent nanoscale phenomena arising from complex interactions. Access to the underlying degrees-of-freedom on their natural time scales motivates the use of advanced ultrafast probes sensitive to self-organised atomic-scale patterns. Here, we report the ultrafast investigation of TaTe 2 , which exhibits unique charge and lattice trimer order characterised by a transition upon cooling from stripe-like chains into a (3 × 3) superstructure of trimer clusters. Utilising MeV-scale ultrafast electron diffraction, we capture the photo-induced TaTe 2 structural dynamics – exposing a rapid ≈ 1.4 ps melting of its low-temperature ordered state followed by recovery via thermalisation into a hot cluster superstructure. Density-functional calculations indicate that the initial quench is triggered by intra-trimer Ta charge transfer which destabilises the clusters, unlike melting of charge density waves in other TaX 2 compounds. Our work paves the way for further exploration and ultimately rapid optical and electronic manipulation of trimer superstructures.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Study of charged-particle emission in neutron reactions on 10 B

The 10 B + n system has been studied by measuring charged particles from neutron-induced reactions in the 1 to 20 MeV energy range. Protons, deuterons, tritons, and α particles were measured at four angles using the pulsed white neutron spectrum at the Los Alamos Neutron Science Center Weapons Neutron Research facility. Differential cross sections for each species are reported. These new data are combined with literature data in an R-matrix analysis of the 11 B compound system. Furthermore, a comparison is made to the molecular and cluster states candidates observed in these reactions.

43 PARTICLE ACCELERATORS↗
DOE OSTI2023

High‐Spin and Reactive Fe 13 Cluster with Exposed Metal Sites

Abstract Atomically defined large metal clusters have applications in new reaction development and preparation of materials with tailored properties. Expanding the synthetic toolbox for reactive high nuclearity metal complexes, we report a new class of Fe clusters, Tp* 4 W 4 Fe 13 S 12 , displaying a Fe 13 core with M−M bonds that has precedent only in main group and late metal chemistry. M 13 clusters with closed shell electron configurations can show significant stability and have been classified as superatoms. In contrast, Tp* 4 W 4 Fe 13 S 12 displays a large spin ground state of S =13. This compound performs small molecule activations involving the transfer of up to 12 electrons resulting in significant cluster rearrangements.

Scott, Anna G.↗
DOE OSTI2023

High-Spin and Reactive Fe 13 Cluster with Exposed Metal Sites

We report atomically defined large metal clusters have applications in new reaction development and preparation of materials with tailored properties. Expanding the synthetic toolbox for reactive high nuclearity metal complexes, we report a new class of Fe clusters, Tp* 4 W 4 Fe 13 S 12 , displaying a Fe 13 core with M-M bonds that has precedent only in main group and late metal chemistry. M 13 clusters with closed shell electron configurations can show significant stability and have been classified as superatoms. In contrast, Tp* 4 W 4 Fe 13 S 12 displays a large spin ground state of S=13. This compound performs small molecule activations involving the transfer of up to 12 electrons resulting in significant cluster rearrangements.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗