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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 217 records · Page 12
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Targeted sulfur(VI) fluoride exchange-mediated covalent modification of a tyrosine residue in the catalytic pocket of tyrosyl-DNA phosphodiesterase 1

Abstract Developing effective inhibitors of the DNA repair enzyme tyrosyl-DNA phosphodiesterase 1 (TDP1) has been challenging because of the enzyme shallow catalytic pocket and non-specific substrate binding interactions. Recently, we discovered a quinolone-binding hot spot in TDP1’s active site proximal to the evolutionary conserved Y204 and F259 residues that position DNA. Sulfur (VI) fluoride exchange (SuFEx) is a biocompatible click chemistry reaction that enables acylation of protein residues, including tyrosine. Selective protein modifications can provide insights into the biological roles of proteins and inform ligand design. As we report herein, we used SuFEx chemistries to prepare covalent TDP1-bound binders showing site-specific covalent bonds with Y204. Our work presents the first application of SuFEx chemistries to TDP1 ligands. It validates the ability to covalently modify specific TDP1 residues by designed targeting and adds to the chemical biology resource toolbox for studying TDP1.

Chemistry↗
DOE OSTI2025

Action painting under spectroscopic light: Excited-state exchange interactions behind the vibrant blue in Jackson Pollock’s Number 1A, 1948

Number 1A, 1948 by Jackson Pollock is a quintessential example of his action painting technique where ropes of color, drips of black, and pools of white coalesce into the layered dynamism that defines his style. While past work has identified the red and yellow pigments that form part of his core palette, the vibrant blue in the painting has remained unassigned. In this study resonance Raman spectroscopy is used to assign the blue in the painting as manganese blue. This assignment offers critical context for the conservation of his works. Importantly, assignment of this pigment enables spectroscopic investigation of the electronic structure origin of the pure hue of manganese blue and the chemical phenomena that produce its color. To probe these phenomena, resonance Raman data are coupled to magnetic circular dichroism spectroscopy and density functional theory calculations to assign and analyze the two electronic transitions that create the blue color. This study reveals these bands are split by excited-state exchange interactions; the gap between them contains the reflected light that gives manganese blue its appearance. This sheds light on distinct advantages of molecular inorganic pigments: their ability to leverage ligand field effects in charge transfer states to create multiple intense visible absorption features and the ability to fine-tune pigment color through host lattice electrostatics.

DFT↗
DOE OSTI2026

Chelation-Driven Chemistry Controls Dissolution Pathways for Facile Critical Mineral Recovery from Ultramafic Resources

The efficient recovery of critical minerals, such as nickel (Ni) and manganese (Mn) from the subsurface is of vital importance, given their role in modern technologies ranging from batteries to advanced alloys. This study explores an approach that employs chelation to enhance critical mineral recovery from ultramafic rocks using chelating ligands under ambient pressures and systematically evaluates the extraction process for the first time. Experimental results demonstrate the superior performance of EDTA and PrDTA in achieving high extraction efficiencies for both Ni and Mn. To further highlight the ability for optimization, the fluid exchange and variation of fluid-to-rock ratio experiments were conducted, revealing tunable controls for engineering recovery. We show that under optimized conditions, a Ni extraction efficiency of ?82% and a Mn extraction efficiency of ~60% is achieved at ambient pressures, which is equivalent to over 23 times the current global Ni production, and 2 million metric tonnes (MMT) greater than the current global Mn production. From both in-situ and ex-situ mining perspectives, the results highlight the potential of chelation to advance sustainable mineral processing. Overall, this work highlights the environmental benefits of innovative ligand-assisted recovery methods, addressing the critical need for the efficient utilization of olivine resources.

Krishnan, Keerthana↗
DOE OSTI2019

Oscillatory cAMP signaling rapidly alters H3K4 methylation

Epigenetic variation reflects the impact of a dynamic environment on chromatin. However, it remains elusive how environmental factors influence epigenetic events. Here, we show that G protein–coupled receptors (GPCRs) alter H3K4 methylation via oscillatory intracellular cAMP. Activation of Gs-coupled receptors caused a rapid decrease of H3K4me3 by elevating cAMP, whereas stimulation of Gi-coupled receptors increased H3K4me3 by diminishing cAMP. H3K4me3 gradually recovered towards baseline levels after the removal of GPCR ligands, indicating that H3K4me3 oscillates in tandem with GPCR activation. cAMP increased intracellular labile Fe(II), the cofactor for histone demethylases, through a non-canonical cAMP target—Rap guanine nucleotide exchange factor-2 (RapGEF2), which subsequently enhanced endosome acidification and Fe(II) release from the endosome via vacuolar H + -ATPase assembly. Removing Fe(III) from the media blocked intracellular Fe(II) elevation after stimulation of Gs-coupled receptors. Iron chelators and inhibition of KDM5 demethylases abolished cAMP-mediated H3K4me3 demethylation. Taken together, these results suggest a novel function of cAMP signaling in modulating histone demethylation through labile Fe(II).

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Magnetic coupling between Fe(NO) spin probe ligands through diamagnetic Ni II , Pd II and Pt II tetrathiolate bridges

Reaction of the nitrosylated-iron metallodithiolate ligand, paramagnetic (NO)Fe(N 2 S 2 ), with [M(CH 3 CN) n ][BF 4 ] 2 salts (M = Ni II , Pd II , and Pt II ; n = 4 or 6) affords di-radical tri-metallic complexes in a stairstep type arrangement ([FeMFe] 2+ , M = Ni, Pd, and Pt), with the central group 10 metal held in a MS 4 square plane. These isostructural compounds have nearly identical ν(NO) stretching values, isomer shifts, and electrochemical properties, but vary in their magnetic properties. Despite the intramolecular Fe∙∙∙Fe distances of ca. 6 Å, antiferromagnetic coupling is observed between {Fe(NO)} 7 units as established by magnetic susceptibility, EPR, and DFT studies. The superexchange interaction through the thiolate sulfur and central metal atoms is on the order of Ni II < Pd II $\ll$ Pt II with exchange coupling constants (J) of -3, -23, and -124 cm -1 , consistent with increased covalency of the M–S bonds (3d < 4d < 5d). This trend is reproduced by DFT calculations with molecular orbital analysis providing insight into the origin of the enhancement in the exchange interaction. Specifically, the magnitude of the exchange interaction correlates surprisingly well with the energy difference between the HOMO and HOMO-1 orbitals of the triplet states, which is reflected in the central metal's contribution to these orbitals. These results demonstrate the ability of sulfur-dense metallodithiolate ligands to engender strong magnetic communication by virtue of their enhanced covalency and polarizability.

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

Identification of structural transitions in bacterial fatty acid binding proteins that permit ligand entry and exit at membranes

Fatty acid (FA) transfer proteins extract FA from membranes and sequester them to facilitate their movement through the cytosol. Detailed structural information is available for these soluble protein–FA complexes, but the structure of the protein conformation responsible for FA exchange at the membrane is unknown. Staphylococcus aureus FakB1 is a prototypical bacterial FA transfer protein that binds palmitate within a narrow, buried tunnel. Here, we define the conformational change from a “closed” FakB1 state to an “open” state that associates with the membrane and provides a path for entry and egress of the FA. Using NMR spectroscopy, we identified a conformationally flexible dynamic region in FakB1, and X-ray crystallography of FakB1 mutants captured the conformation of the open state. In addition, molecular dynamics simulations show that the new amphipathic α-helix formed in the open state inserts below the phosphate plane of the bilayer to create a diffusion channel for the hydrophobic FA tail to access the hydrocarbon core and place the carboxyl group at the phosphate layer. The membrane binding and catalytic properties of site-directed mutants were consistent with the proposed membrane docked structure predicted by our molecular dynamics simulations. Finally, the structure of the bilayer-associated conformation of FakB1 has local similarities with mammalian FA binding proteins and provides a conceptual framework for how these proteins interact with the membrane to create a diffusion channel from the FA location in the bilayer to the protein interior.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Machine learning and ligand binding predictions: A review of data, methods, and obstacles

We report that computational predictions of ligand binding is a difficult problem, with more accurate methods being extremely computationally expensive. The use of machine learning for drug binding predictions could possibly leverage the use of biomedical big data in exchange for time-intensive simulations. This paper reviews current trends in the use of machine learning for drug binding predictions, data sources to develop machine learning algorithms, and potential problems that may lead to overfitting and ungeneralizable models. A few popular datasets that can be used to develop virtual high-throughput screening models are characterized using spatial statistics to quantify potential biases. We can see from evaluating some common benchmarks that good performance correlates with models with high-predicted bias scores and models with low bias scores do not have much predictive power. A better understanding of the limits of available data sources and how to fix them will lead to more generalizable models that will lead to novel drug discovery.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Development of $\mathrm{AMOEBA}$ Polarizable Force Field for Rare-Earth La 3+ Interaction with Bioinspired Ligands

Rare-earth metals (REMs) are crucial for many important industries, such as power generation and storage, in addition to cancer treatment and medical imaging. One promising new REM refinement approach involves mimicking the highly selective and efficient binding of REMs observed in relatively recently discovered proteins. However, realizing any such bioinspired approach requires an understanding of the biological recognition mechanisms. In this report we developed a new classical polarizable force field based on the AMOEBA framework for modeling a lanthanum ion (La 3+ ) interacting with water, acetate, and acetamide, which have been found to coordinate the ion in proteins. The parameters were derived by comparing to high-level ab initio quantum mechanical (QM) calculations that include relativistic effects. The AMOEBA model, with advanced atomic multipoles and electronic polarization, is successful in capturing both the QM distance-dependent La 3+ –ligand interaction energies and experimental hydration free energy. A new scheme for pairwise polarization damping (POLPAIR) was developed to describe the polarization energy in La 3+ interactions with both charged and neutral ligands. Simulations of La3+ in water showed water coordination numbers and ion–water distances consistent with previous experimental and theoretical findings. Water residence time analysis revealed both fast and slow kinetics in water exchange around the ion. This new model will allow investigation of fully solvated lanthanum ion–protein systems using GPU-accelerated dynamics simulations to gain insights on binding selectivity, which may be applied to the design of synthetic analogues.

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

Structural mechanisms for binding and activation of a contact-quenched fluorophore by RhoBAST

The fluorescent light-up aptamer RhoBAST, which binds and activates the fluorophore–quencher conjugate tetramethylrhodamine-dinitroaniline with high affinity, super high brightness, remarkable photostability, and fast exchange kinetics, exhibits excellent performance in super-resolution RNA imaging. Here we determine the co-crystal structure of RhoBAST in complex with tetramethylrhodamine-dinitroaniline to elucidate the molecular basis for ligand binding and fluorescence activation. The structure exhibits an asymmetric “A”-like architecture for RhoBAST with a semi-open binding pocket harboring the xanthene of tetramethylrhodamine at the tip, while the dinitroaniline quencher stacks over the phenyl of tetramethylrhodamine instead of being fully released. Molecular dynamics simulations show highly heterogeneous conformational ensembles with the contact-but-unstacked fluorophore–quencher conformation for both free and bound tetramethylrhodamine-dinitroaniline being predominant. The simulations also show that, upon RNA binding, the fraction of xanthene-dinitroaniline stacked conformation significantly decreases in free tetramethylrhodamine-dinitroaniline. This highlights the importance of releasing dinitroaniline from xanthene tetramethylrhodamine to unquench the RhoBAST–tetramethylrhodamine-dinitroaniline complex. Using SAXS and ITC, we characterized the magnesium dependency of the folding and binding mode of RhoBAST in solution and indicated its strong structural robustness. The structures and binding modes of relevant fluorescent light-up aptamers are compared, providing mechanistic insights for rational design and optimization of this important fluorescent light-up aptamer-ligand system.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Advances in Operando Electrocatalysis with High-Resolution Hard X-Ray Spectroscopy

Electrocatalysis unfolds at the interface—where solids, liquids, and gases meet to exchange charge, transform molecules, and set the foundation for technologies like CO 2 conversion, and water splitting. These interfacial regions are inherently dynamic, chemically diverse, and structurally heterogeneous. How atoms rearrange, oxidize, coordinate ligands, or adsorb reaction intermediates under electro-chemical potential defines a catalyst’s performance. Furthermore, capturing these changes with element specificity and electronic sensitivity under operando conditions remains one of the most critical challenges in the field.

Garcia-Esparza, Angel T. [SLAC National Accelerato↗
DOE OSTI2026

Magnetic and EPR Spectroscopic Studies of Thiolate Bridged Divalent Ni, Pd, and Pt Ions Capped with VO(N 2 S 2 ) Metalloligands

Reactions of the metallodithiolate complex VO(bme-dach) (hereafter abbreviated as V, where bme-dach = N,N ′-bis(2-mercaptoethyl)-1,4-diazacycloheptane) with [Pd II (CH 3 CN) 4 ](BF 4 ) 2 and [Pt II (CH 3 CN) 4 ](BF 4 ) 2 yield the V–M–V trimetallic compounds [VPdV](BF 4 ) 2 (2) and [VPtV](BF 4 ) 2 (3). Reaction of a similar metalloligand, VO(bme-daco) (hereafter abbreviated as V′ where bme-daco = N,N′-bis(2-mercaptoethyl)-1,5-diazacyclooctane) with [Ni II (CH 3 CN) 6 ](BF 4 ) 2 afforded the related salt [V′NiV′](BF 4 ) 2 (1). X-ray structural analyses revealed that cations in 1, 2, and 3 adopt a stairstep C 2h structure consisting of two terminal VO(N 2 S 2 ) moieties bridged via thiolate sulfur to the group 10 metal ions. Weak ferromagnetic superexchange coupling (J = 0.282 cm –1 for 1, 0.954 cm –1 for 2, and 1.372 cm –1 for 3) was observed between the two S = 1/2 V IV centers separated by distances in the range of 5.9–6.3 Å, with J values varying following the order Ni < Pd < Pt. Frozen-solution EPR spectra measured on the more soluble [BArF 24 ] − (BArF 24 – = tetrakis((3,5-trifluoromethyl)phenyl)borate) analogues revealed that the [VPtV] 2+ cation exhibits a 15-line hyperfine splitting of 225 MHz at g = 4 in parallel mode, confirming exchange coupling between the two 51 V, I = 7/2 nuclei. Density-functional theory (DFT) calculations indicate an S = 1 ground state for 1–3. These results demonstrate that the choice of paramagnetic metallodithiolate ligand and diamagnetic bridge in such trimetallic species influences the sign and magnitude of magnetic interactions.

anions↗
DOE OSTI2024

Inducing Ferrimagnetic Exchange in 1D-FeSe 2 Chains Using Heteroleptic Amine Complexes: [Fe(en)(tren)][FeSe 2 ] 2

[Fe(en)(tren)][FeSe 2 ] 2 (en = ethylenediamine, C 2 H 8 N 2 , tren = tris(2-aminoethyl)amine, C 6 H 18 N 4 ) has been synthesized by a mixed-ligand solvothermal method. Its crystal structure contains heteroleptic [Fe(en)(tren)] 2+ complexes with distorted octahedral coordination, incorporated between 1D-FeSe 2 chains composed of edge–sharing FeSe 4 tetrahedra. The twisted octahedral coordination environment of the Fe–amine complex leads to partial dimerization of Fe–Fe distances in the FeSe 2 chains so that the FeSe 4 polyhedra deviate strongly from the regular tetrahedral geometry. 57 Fe Mössbauer spectroscopy reveals oxidation states of +3 for the Fe chain atoms and +2 for the Fe complex atoms. The close proximity of Fe atoms in the chains promotes ferromagnetic nearest neighbor interactions, as indicated by a positive Weiss constant, θ = +53.8(6) K, derived from the Curie–Weiss fitting. Magnetometry and heat capacity reveal two consecutive magnetic transitions below 10 K. DFT calculations suggest that the ordering observed at 4 K is due to antiferromagnetic intrachain interactions in the 1D-FeSe 2 chains. The combination of two different ligands creates an asymmetric coordination environment that induces changes in the structure of the Fe–Se fragments. Finally, this synthetic strategy opens new ways to explore the effects of ligand field strength on the structure of both Fe-amine complexes and surrounding Fe–Se chains.

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

Cooperative Lanthanide Solvation in an Ionic Liquid for Critical Materials Separations

Effectively separating critical materials, including intra-lanthanide separations, is crucial for meeting growing application demands. Liquid–liquid extraction (LLE) is the industry standard for lanthanide separations, where the selectivity can depend on small changes in metal coordination. In this work, we investigate representative lanthanide Eu coordination with a neutral malonamide extractant in an imidazolium bistriflimide ionic liquid (IL) solvent. Through systematic titrations of the water and extractant and under extraction conditions, we observe surprising cooperative Eu solvation with the IL anion and extractant. Time-resolved fluorescence spectroscopy measurements show strong extractant coordination in water-saturated IL. Lifetime measurements show no water coordination, and extended X-ray fine structure spectroscopy data provide a coordination number of 10. Molecular dynamics simulations confirm this coordination number and reveal IL anion coordination in the final Eu complex, even though it is ordinarily a significantly weaker ligand compared to water. The lack of water in the final extracted complex and IL anion coordination potentially explain the increased extraction in LLE systems using ILs, as evidenced by higher distribution ratios for cation exchange extraction, despite the energetic cost of cation transfer to the aqueous phase. These results highlight the opportunities for tuning metal coordination to drive extraction in unique solvent systems.

Carr, Amanda J.↗
DOE OSTI2025

DeSelenator: A Se-Removal Process for Environmental Decontamination of Wastewaters from Coal-Burning Power Plants

Selenium may become a toxic contaminant of freshwater systems when released into the environment through industrial wastewaters from mining, coal-burning power plants, or oil refining. Efficient and cost-effective Se-removal technologies are therefore necessary to reduce Se concentrations in these wastewaters to below the regulatory discharge limits. In this study, we have demonstrated an effective process that removes Se, mostly as selenate anions, from wastewaters generated by coal-burning power plants. This process, dubbed DeSelenator, leverages the high concentration of sulfate relative to selenate in the wastewater and the propensity of these oxyanions to cocrystallize with benzene-bis-iminoguanidinium (BBIG) cations into extremely insoluble salts (on par with BaSO 4 ). The SO 4 2− /SeO 4 2− cocrystallization with BBIG removes over 90% of S and Se from the wastewater. Following removal of the precipitate by filtration, the filtrate is passed over an anion-exchange resin that further reduces selenium concentration to 5 ppb, the EPA’s regulatory limit for freshwater systems. Finally, the effluent is passed over an activated carbon column, which removes 99.8% of the residual BBIG ligand remaining after crystallization, allowing for the safe discharge of the treated water into the environment. The Se-removal process was first optimized in the lab at the bench scale and then tested in the field at the Tennessee Valley Authority’s Bull Run coal-burning power plant. A technoeconomic assessment found the cost of water treatment with DeSelenator is on par with that of the active biological method, which is currently considered a state-of-the-art Se-removal technology.

anions↗
DOE OSTI2025

Crystal field splittings and magnetic ground state of the square-lattice antiferromagnets YbBi 2 ⁢ClO 4 and YbBi 2 ⁢IO 4 with J eff = $\frac{1}{2}$

Here, we report on the crystal field level splitting and magnetic ground state of the J eff = $\frac{1}{2}$ square lattice antiferromagnets YbBi 2 ⁢ClO 4 and YbBi 2 ⁢IO 4 using powder inelastic neutron scattering (INS) and neutron diffraction measurements. Both compounds exhibit a well-isolated Γ 7 doublet ground state under a tetragonal crystal field environment, confirming a robust J eff = $\frac{1}{2}$ picture with slight XY-type anisotropic character in the g-tensor. Notably, the ground state wave functions closely resemble the Γ 7 doublet expected in the perfect cubic limit, consistent with the nearly cubic ligand configuration of eight O 2- ions surrounding Yb 3+ . Below T N = 0.21 K, YbBi 2 ⁢IO 4 exhibits a stripe long-range magnetic order characterized by an ordering wave vector q m = (1/2, 0, 0) or its symmetry-equivalent (0, 1/2, 0), with magnetic moments aligned along q m . The ordered moment is approximately 79% of the classical prediction, significantly larger than expected from the isotropic J 1 -J 2 model, suggesting the possible involvement of exchange anisotropy in explaining this observation. We show that symmetry-allowed XXZ and bond-dependent anisotropic exchange terms in a square lattice can play a critical role in stabilizing the stripe order and suppressing the moment reduction as observed. These findings establish YbBi 2 ⁢ClO 4 and YbBi 2 ⁢IO 4 as unique platforms for exploring rich J eff = $\frac{1}{2}$ magnetism from two less investigated perspectives: (i) on a square lattice and (ii) within a (nearly) cubic ligand environment.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2025

Bulk Anion Recognition Kinetically Holds Back Interfacial Adsorption

The competition between bulk and interfacial phenomena underlies many key processes in complex chemical phenomena and transport. While competitive processes are often framed in a thermodynamic context, opportunities to leverage transient species found away from equilibrium can provide a kinetic handle to achieve unconventional reaction outcomes. In this work, we outfit an iminoguanidinium headgroup capable of selective SO 4 2– complexation with alkyl tails of varying complexity to probe competitive bulk and interfacial reaction pathways and tune kinetic pathways for selective chemical separations. Using sum frequency generation (SFG) vibrational spectroscopy we unexpectedly find that adsorption of ligands to the air–aqueous interface was dramatically slowed down for species with increasingly hydrophobic tails. Underlying this phenomenon, we show that the formation of bulk colloidal species with differing propensities for SO 4 2– inhibited surface adsorption via a kinetic bottleneck in the exchange of molecular extractants with colloidal aggregates. This kinetic effect could open up avenues to access unconventional selectivity via complexation of strongly coordinating species in the bulk phase, allowing for more weakly coordinating species to transport via interfacial mechanisms. Furthermore, this work broadly probes nonequilibrium phenomena in chemical separations that arise through unexpected interfacial events that are neglected in traditional equilibrium descriptions.

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

Multistage Condensation Pathway Minimizes Hysteresis in Water Harvesting with Large-Pore Metal–Organic Frameworks

Metal-organic frameworks (MOFs) have emerged as promising materials for atmospheric water harvesting (AWH). Large-pore MOFs provide high water capacity, but their significant hysteresis between sorption and desorption makes them unsuitable for AWH. Co2Cl2(BTDD) is a noteworthy exception. This MOF has large, 2.2 nm diameter one-dimensional pores, and combines both record-high water capacity and minimal hysteresis, making it an excellent material for water capture in arid areas. Sorption reversibility in Co2Cl2(BTDD) has been attributed to continuous water uptake. However, the sharp adsorption/desorption in the isotherms supports a discontinuous first-order transition. Here we use molecular simulations to compute the water adsorption and desorption pathways and isotherms in a Co2Cl2(BTDD) model, to elucidate how does this MOF achieve reversibility despite its large pore size. The simulations reveal a multi-stage mechanism of discontinuous water uptake facilitated by spatial segregation of rows of hydrophilic metal sites bridged by ~1 nm hydrophobic ligands. The multi-stage mechanism breaks the barrier of capillary condensation into smaller, easier to surmount ones, resulting in a facile process despite the sharp density discontinuity between confined liquid and vapor. Our results explain why exchanging Co2+ for Ni2+ or Clfor F- in the MOF have minimal impact on the condensation and desorption pressures. On the other hand, we predict that a decrease in hydrophilicity of the MOF vertices would strongly increase the hysteresis. We expect that the relationships between spatial distribution of hydrophilic sites and hysteresis unraveled in this study assist the design of water harvesting materials with maximal capacity and reversibility.

Zaragoza, Alberto↗