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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
NASA NTRS1991

The binding energies of Cu(+)-(H2O)n and Cu(+)-(NH3)n (n = 1-4)

The successive binding energies of up to four H2O and NH3 ligands to Cu(+) are computed at the self-consistent-field and modified coupled-pair functional levels. The most stable structures are those where all ligands are equivalent. Replacing Cu(+) by a point charge gives binding energies that are in good agreement with ab initio and experimental results, and is consistent with bonding that is largely charge dipole in nature. About two-thirds of the large reduction in ligand binding energy between the second and third ligand is due to ligand-ligand repulsion, while one-third is due to increased metal-ligand repulsion resulting from a loss of sd-sigma hybridization. The first and second ligand binding energies increase substantially at the correlated level due to an improved description of sd-sigma hybridization.

Bauschlicher, Charles W., Jr.↗
DOE OSTI2025

Designing the Nanoconfined Environment for Energy-Efficient Metal Nanoparticle/Ligand-Based Electrocatalysts

Nanoconfined electrocatalysts demonstrate enhanced selectivity and activity owing to new phenomena emerging from chemical species confined at the interface. Creating these nanoconfined pockets at the interface is not trivial. We need highly negative potentials to create the pockets in metal/ligand catalysts like Ag-nanoparticle/ordered ligand interlayer catalysts. Lowering this activation potential can make the electrocatalysis more energy-efficient, and changes in the environment can impact this potential. We used Density Functional Theory (DFT) to evaluate the impact of ligand length and density, interfacial protons, and surface defects like Ag vacancies and Cu and Au dopants. The nanoconfined configuration is stabilized when the ligands are longer and more densely packed, leading to better agglomeration. It is also stabilized when the ligands adsorb protons and when the ligands detach from the surface easily owing to lower charge transfer. Au-doped surfaces displayed the lowest charge transfer and decreased the activation potential.

Jana, Asmita↗
DOE OSTI2021

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

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

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

Designing nanoparticle interfaces for inner-sphere catalysis

Interfaces are an intrinsic component of nanoparticle catalysts and play a critical role in directing their function. Our understanding of the complexity of the nanoparticle interface and how to manipulate it at the molecular level has advanced significantly in recent years. Given this, attention is shifting towards the creation of designer nanoparticle interfaces that impact the activity and direct the mechanisms of inner-sphere catalytic reactions. In this perspective, we seek to highlight and contextualize these efforts. First, methods to alter nanoparticle surfaces are presented, including annealing and plasma treating, as well as more mild chemical treatments, including ligand exchange, etching, and addition (via covalent functionalization). Then interfacial chemistry developed to alter catalytic activity, selectivity, and reaction environment will be highlighted. Finally, we look forward to the challenges that remain to be overcome for realizing the true potential of colloidal nanoparticle catalysis.

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

Half‐sandwich ruthenium complex with a very low overpotential and excellent activity for water oxidation under acidic conditions

Abstract Molecular catalysts are acknowledged for the ability to design reaction sites within well‐defined structures to achieve high catalytic activities. However, in many cases, molecular catalysts undergo structural changes to some other form(s), which are finally the real catalysts. Here, we report two half‐sandwich ruthenium complexes; [Ru([9]aneN3)(bpy)Cl] + 3 and [Ru([9]aneN3)(pic)OH 2 ] 2+ 4 , based on the macrocyclic 1,4,7‐triazacyclononane ([9]aneN3) ligand for water oxidation (WO). The two complexes have similar core but different ancillary ligands, which greatly affected their stability as well as activity for WO. Complex 3 retained high stability and excellent activity (turnover number [TON] = 1250) in chemical WO and first‐order reaction kinetics with respect to [Ce IV ] with a calculated rate constant ( k cat ) of 34.59 s −1 . Further, the complex demonstrated very low overpotential of ~210 mV in electrochemical WO. At an overpotential of only 400 mV, turnover frequency (TOF) of complex 3 was electrochemically estimated to be 131.2 s −1 . In contrast, complex 4 underwent picolinate ligand dissociation, as a deactivation pathway, to form the tri‐aqua derivative. Density functional theory (DFT) calculations are used to explain the dissociation mechanism of picolinate ligand in complex 4 , which happens through a stepwise dissociation mechanism.

Younus, Hussein A.↗
DOE OSTI2022

Ligand-coordination effects on the selective hydrogenation of acetylene in single-site Pd-ligand supported catalysts

The selective hydrogenation of acetylene to ethylene is a critical step in the synthesis of polyethylenes. Achieving high conversion to ethylene without over-hydrogenation to ethane is a challenge that requires control of the transition metal site, which we achieve through a ligand-coordinated supported catalyst (LCSC) strategy. Using Pd catalysts coordinated to 1,10-phenanthroline-5,6-dione (PDO) ligands on CeO2 supports, we have discovered that the reaction selectivity depends strongly on the ligand:metal ratio with higher selectivity when more ligand is present in the catalyst. Catalyst structure was examined by extended X-ray absorption fine structure spectroscopy, transmission electron microscopy, and CO adsorption, which indicate single-atom character of the Pd. The ligand:metal ratio is determined by Xray photoelectron spectroscopy measurements and correlated with hydrogenation reactions under steady-state flow conditions to examine trends in hydrogenation activity and selectivity. Those trends can be better understood by density functional theory calculations that indicate hydrogen binding on the ligand to guide reaction selectivity toward the desired ethylene hydrogenation product. Here these results demonstrate the importance of considering the dynamic character of LCSCs and inform the design of future single-site heterogeneous catalysts.

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

Operando Elucidation on the Working State of Immobilized Fluorinated Iron Porphyrin for Selective Aqueous Electroreduction of CO 2 to CO

Iron porphyrin-based molecular catalysts can electrocatalyze CO 2 reduction to CO at nearly 100% selectivity in water. Nevertheless, the associated active sites and reaction mechanisms remain debatable, impeding the establishment of design guidelines for effective catalysts. This study reports coupling in operando experiments and theoretical calculations for immobilized 5,10,15,20-tetrakis(pentafluorophenyl) porphyrin Fe(III) chloride (FeF 20 TPP) for electrocatalytic CO 2 reduction in an aqueous phase. In operando UV–vis and X-ray absorption near-edge structure spectra indicated the persisting presence of Fe(II) species during the cathodic reaction, acting as catalytic sites that accommodate CO as Fe(II)–CO adducts. Consistently, the density functional calculations pointed out that the ligand-reduced state with oxidized Fe, namely, [Fe(II)F 20 (TPP • )] - , prevails in the catalytic cycle prior to the rate-controlling step. This work provides the conclusive representation related to the working states of Fe-based molecular catalysts under reaction conditions.

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

Ligand efficacy shifts a nuclear receptor conformational ensemble between transcriptionally active and repressive states

Abstract Nuclear receptors (NRs) are thought to dynamically alternate between transcriptionally active and repressive conformations, which are stabilized upon ligand binding. Most NR ligand series exhibit limited bias, primarily consisting of transcriptionally active agonists or neutral antagonists, but not repressive inverse agonists—a limitation that restricts understanding of the functional NR conformational ensemble. Here, we report a NR ligand series for peroxisome proliferator-activated receptor gamma (PPARγ) that spans a pharmacological spectrum from repression (inverse agonism) to activation (agonism) where subtle structural modifications switch compound activity. While crystal structures provide snapshots of the fully repressive state, NMR spectroscopy and conformation-activity relationship analysis reveals that compounds within the series shift the PPARγ conformational ensemble between transcriptionally active and repressive conformations that are natively populated in the apo/ligand-free ensemble. Our findings reveal a molecular framework for minimal chemical modifications that enhance PPARγ inverse agonism and elucidate their influence on the dynamic PPARγ conformational ensemble.

Science & Technology - Other Topics↗
DOE OSTI2022

Decoding the protein–ligand interactions using parallel graph neural networks

Abstract Protein–ligand interactions (PLIs) are essential for biochemical functionality and their identification is crucial for estimating biophysical properties for rational therapeutic design. Currently, experimental characterization of these properties is the most accurate method, however, this is very time-consuming and labor-intensive. A number of computational methods have been developed in this context but most of the existing PLI prediction heavily depends on 2D protein sequence data. Here, we present a novel parallel graph neural network (GNN) to integrate knowledge representation and reasoning for PLI prediction to perform deep learning guided by expert knowledge and informed by 3D structural data. We develop two distinct GNN architectures: $$\hbox {GNN}_{\mathrm{F}}$$ GNN F is the base implementation that employs distinct featurization to enhance domain-awareness, while $$\hbox {GNN}_{\mathrm{P}}$$ GNN P is a novel implementation that can predict with no prior knowledge of the intermolecular interactions. The comprehensive evaluation demonstrated that GNN can successfully capture the binary interactions between ligand and protein’s 3D structure with 0.979 test accuracy for $$\hbox {GNN}_{\mathrm{F}}$$ GNN F and 0.958 for $$\hbox {GNN}_{\mathrm{P}}$$ GNN P for predicting activity of a protein–ligand complex. These models are further adapted for regression tasks to predict experimental binding affinities and $$\hbox {pIC}_{\mathrm{50}}$$ pIC 50 crucial for compound’s potency and efficacy. We achieve a Pearson correlation coefficient of 0.66 and 0.65 on experimental affinity and 0.50 and 0.51 on $$\hbox {pIC}_{\mathrm{50}}$$ pIC 50 with $$\hbox {GNN}_{\mathrm{F}}$$ GNN F and $$\hbox {GNN}_{\mathrm{P}}$$ GNN P , respectively, outperforming similar 2D sequence based models. Our method can serve as an interpretable and explainable artificial intelligence (AI) tool for predicted activity, potency, and biophysical properties of lead candidates. To this end, we show the utility of $$\hbox {GNN}_{\mathrm{P}}$$ GNN P on SARS-Cov-2 protein targets by screening a large compound library and comparing the prediction with the experimentally measured data.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Crystal structure of domain of unknown function 507 (DUF507) reveals a new protein fold

The crystal structure of the domain of unknown function family 507 protein from Aquifex aeolicus is reported (AaDUF507, UniProt O67633, 183 residues). The structure was determined in two space groups (C222 1 and P3 2 21) at 1.9 Å resolution. The phase problem was solved by molecular replacement using an AlphaFold model as the search model. AaDUF507 is a Y-shaped α-helical protein consisting of an anti-parallel 4-helix bundle base and two helical arms that extend 30-Å from the base. The two crystal structures differ by a 25° rigid body rotation of the C-terminal arm. The tertiary structure exhibits pseudo-twofold symmetry. The structural symmetry mirrors internal sequence similarity: residues 11–57 and 102–148 are 30% identical and 53% similar with an E-value of 0.002. In one of the structures, electron density for an unknown ligand, consistent with nicotinamide or similar molecule, may indicate a functional site. Docking calculations suggest potential ligand binding hot spots in the region between the helical arms. Structure-based query of the Protein Data Bank revealed no other protein with a similar tertiary structure, leading us to propose that AaDUF507 represents a new protein fold.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Structures of TGF-β with betaglycan and signaling receptors reveal mechanisms of complex assembly and signaling

Abstract Betaglycan (BG) is a transmembrane co-receptor of the transforming growth factor-β (TGF-β) family of signaling ligands. It is essential for embryonic development, tissue homeostasis and fertility in adults. It functions by enabling binding of the three TGF-β isoforms to their signaling receptors and is additionally required for inhibin A (InhA) activity. Despite its requirement for the functions of TGF-βs and InhA in vivo, structural information explaining BG ligand selectivity and its mechanism of action is lacking. Here, we determine the structure of TGF-β bound both to BG and the signaling receptors, TGFBR1 and TGFBR2. We identify key regions responsible for ligand engagement, which has revealed binding interfaces that differ from those described for the closely related co-receptor of the TGF-β family, endoglin, thus demonstrating remarkable evolutionary adaptation to enable ligand selectivity. Finally, we provide a structural explanation for the hand-off mechanism underlying TGF-β signal potentiation.

Science & Technology - Other Topics↗
DOE OSTI2024

Thermal Activation of Zirconium(IV) Acetylacetonate Catalysts to Enhance Polyurethane Synthesis and Reprocessing

Carbamate formation and exchange catalysts enable efficient polyurethane (PU) manufacturing, as well as emerging recycling and reprocessing methods for PU thermosets. Zirconium β-diketonate complexes, such as Zr acetylacetonate [Zr(acac) 4 ], are effective alternatives to toxic organotin catalysts that have been used for PU reprocessing. Here, we report that Zr(acac) 4 undergoes a thermally activated process in the PU network during reprocessing that transforms it into a more active carbamate exchange catalyst. This process is associated with the irreversible loss of acetylacetonate ligands and is not observed for the more sterically hindered Zr 2,2,6,6-tetramethyl-3,5-heptanedione [Zr(tmhd) 4 ] complex. Crossover experiments between PU thermoplastics indicated enhanced carbamate exchange after the thermal activation of Zr(acac) 4 in the presence of one of the PUs, whereas a sample of Zr(acac) 4 activated in the absence of the PU had no catalytic activity. Thermal gravimetric analysis suggested that this process is associated with the loss of one protonated acac ligand. Stress relaxation analysis of PU thermosets indicated a distinct change in the characteristic relaxation time associated with the thermal activation of Zr(acac) 4 at temperatures above 140 °C; no such change was observed for samples reprocessed using Zr(tmhd) 4 . Density functional theory and molecular experiments suggest that irreversible ligand exchange of acac with alkoxide or carbamate reduces the activation energy for urethane formation and reversion. Furthermore, the Zr(acac) 4 catalyst activated in the presence of a PU’s polyol precursor provided more porous and less dense PU foams compared to those made using the unactivated Zr(acac) 4 catalyst. Furthermore, these findings are important for developing improved PU synthesis and recycling processes. Thermally activating a catalyst during reprocessing may provide more nuanced control of the in-use and reprocessing characteristics of PU thermosets.

Alcohols↗
DOE OSTI2025

Assessing the potential of deep learning for protein–ligand docking

The effects of ligand binding on protein structures and their in vivo functions carry numerous implications for modern biomedical research and biotechnology development efforts such as drug discovery. Although several deep learning (DL) methods and benchmarks designed for protein–ligand docking have recently been introduced, so far no previous works have systematically studied the behaviour of the latest docking and structure prediction methods within the broadly applicable context of: (1) using predicted (apo) protein structures for docking (for example, for applicability to new proteins); (2) binding multiple (cofactor) ligands concurrently to a given target protein (for example, for enzyme design); and (3) having no previous knowledge of binding pockets (for example, for generalization to unknown pockets). To enable a deeper understanding of the real-world utility of docking methods, we introduce PoseBench, a comprehensive benchmark for broadly applicable protein–ligand docking. PoseBench enables researchers to rigorously and systematically evaluate DL methods for apo-to-holo protein–ligand docking and protein–ligand structure prediction using both primary ligand and multiligand benchmark datasets, the latter of which we introduce to the DL community. Empirically, using PoseBench, we find that: (1) DL cofolding methods generally outperform comparable conventional and DL docking baseline algorithms, but popular methods such as AlphaFold 3 are still challenged by prediction targets with new protein–ligand binding poses; (2) certain DL cofolding methods are highly sensitive to their input multiple sequence alignments, whereas others are not; and (3) DL methods struggle to strike a balance between structural accuracy and chemical specificity when predicting new or multiligand protein targets.

Morehead, Alex [Lawrence Berkeley National Laborat↗
DOE OSTI2022

Ligand Coverage and Exciton Delocalization Control Chiral Imprinting in Perovskite Nanoplatelets

Chiral perovskites have generated significant recent interest, yet little is known about how their chiro-optical properties arise. In this study, chiral methylammonium lead halide perovskite nanoplatelets (NPLs) with varied halide and ligand compositions are prepared using direct synthetic methods. Circular dichroism (CD) and 1 H NMR studies find a non-linear relationship between the chiroptical properties and the ratio of chiral phenylethylammonium (PEA) to achiral octylamine (OA) ligands on the NPL surface. We use density functional theory (DFT) computations and a chiral imprinted particle-in-a-box model to rationalize the experimentally observed CD spectra and find that the saturation point of the induced chirality depends on the size of the perovskite exciton relative to the size of the ligands. Temperature-dependent CD and 1 H NMR studies, combined with DFT analysis, show that both the CD intensity and sign depend strongly on the structure and orientation of the ligands. Furthermore, this work reveals the complex nature of chiral imprinting in perovskite nanostructures and establishes a simple physical model for ligand-induced chiral imprinting to guide the further development of chiral materials.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Structure-function studies of Vibrio cholerae quorum-sensing receptor CqsR signal recognition

Ethanolamine signaling through the transmembrane quorum-sensing receptor CqsR influencesVibrio choleraeniche recognition and host colonization. In this study, we present a comprehensive structure-function analysis of CqsR. Specifically, we have determined X-ray crystal structures of the CqsR periplasmic domain bound to the signaling agonist ethanolamine and its analogs, serinol and L-alaninol, as well as the ligand-free (apo) form of CqsR. The periplasmic ligand-binding domain of CqsR is a Cache domain, the most prevalent extracellular sensory module in prokaryotes. Our findings provide a rare structural comparison of ligand-bound and unbound states of a Cache domain receptor. Coupled with thermodynamic binding assays and genetic analyses, these structures elucidate the molecular basis of CqsR ligand specificity. This study not only advances the understanding of Cache domain function but also informs the identification of ligands for orphan Cache receptors and the rational design of signaling agonists and antagonists. Lastly, we discuss ligand-induced conformational changes in the CqsR Cache domains and explore the potential for the existence of additional regulatory ligands.

Microbiology↗
DOE OSTI2023

Multiconfiguration Pair-Density Functional Theory for Vertical Excitation Energies in Actinide Molecules

Modeling actinides with electronic structure theories is challenging because these systems present a strong ligand field and metal–ligand covalency. Here, we systematically investigate the effectiveness of pair-density functional theory (PDFT) for the calculation of vertical excitation energies in An(III), [An III Cl 6 ] 3– , and [An VI O 2 ] 2+ (An = U, Np, Pu, and Am). We compare the performance of PDFT, hybrid PDFT, and multistate PDFT with traditional active-space methods followed by perturbation theory, like multistate CASPT2, and with experimental data. Overall, multistate PDFT gives quantitative agreement with multistate CASPT2 at a significantly reduced computational cost.

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

EPR and 31 P ENDOR Characterization of Pseudo-Jahn–Teller Dynamics and N 2 Activation in Functional Nitrogenase Models, P 3 E M(N 2 ) (M = Fe, Co; E = Si, B, C)

Here, the nominally trigonal, pseudo-Jahn-Teller (PJT)-active, S = ½ N 2 -bound transition-metal complexes, P 3 E M(N 2 ), M = Fe, Co, with three in-plane phosphine-ligands and axial donors, E = Si, B, C, include functional nitrogenase models that catalyze reduction of N 2 to NH 3 . We applied EPR, 31 P ENDOR spectroscopy and DFT computations to characterize the PJT-induced distortions of four selected P 3 E M(N 2 ), revealing how the metal-ion and axial ligand E together tune both PJT dynamics and N 2 activation for reduction. Comparisons reveal an unrecognized correlation between PJT distortion, M-E bond elasticity, and N 2 activation, providing guidelines for designing bioinspired N 2 -reduction catalysts.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗