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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 307 records · Page 17
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Uptake and binding of La 3+ and Cr 3+ ions by alkali metal substituted alpha-zirconium phosphate

The conversion of alpha-zirconium phosphate, Zr(HPO 4 ) 2 ·H 2 O, to the K-, Rb-, and Cs-phases and the subsequent ion exchange behavior of these alkali metal phases, A-ZrP, with La 3+ and Cr 3+ have been investigated. The conversion to the A-ZrP phases was achieved by reaction with metal chloride, metal hydroxide solution, and confirmed through various techniques, including X-ray powder diffraction, thermogravimetry analysis, IR spectroscopy, scanning and transmission electron microscopy, and X-ray photoelectron spectroscopy. The effect of material hydration, which increased the interlayer distance, was also examined. The ion exchange behavior of the A-ZrP showed strong affinity for both La 3+ , a representative for trivalent lanthanide metals, and Cr 3+ , a representative for the trivalent transition metals, with a rapid, near quantitative removal of the M 3+ ions at a pH of 3 when the ion concentration was ≤25% of the ion exchange capacity of the materials. Additionally, the ion affinity was shown to be pH and concentration-dependent, decreasing with a decrease in pH or an increase in ion concentration. Lastly, the binding strength of La- and Cr-loaded ZrP materials was examined through a series of leaching experiments in a carbonate buffer, phosphate buffer, HEPES buffer, and a series of EDTA solutions at various concentrations. No observable leaching occurred in the carbonate buffer, phosphate buffer, HEPES buffer, or when the EDTA concentration was below 0.1 mM. These results highlight the potential for the A-ZrP materials to provide a platform for trivalent transition metal and trivalent lanthanide radionuclide capture for various applications.

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

An ultrapotent synthetic nanobody neutralizes SARS-CoV-2 by stabilizing inactive Spike

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus enters host cells via an interaction between its Spike protein and the host cell receptor angiotensin-converting enzyme 2 (ACE2). By screening a yeast surface-displayed library of synthetic nanobody sequences, we developed nanobodies that disrupt the interaction between Spike and ACE2. Cryo–electron microscopy (cryo-EM) revealed that one nanobody, Nb6, binds Spike in a fully inactive conformation with its receptor binding domains locked into their inaccessible down state, incapable of binding ACE2. Affinity maturation and structure-guided design of multivalency yielded a trivalent nanobody, mNb6-tri, with femtomolar affinity for Spike and picomolar neutralization of SARS-CoV-2 infection. mNb6-tri retains function after aerosolization, lyophilization, and heat treatment, which enables aerosol-mediated delivery of this potent neutralizer directly to the airway epithelia.

60 APPLIED LIFE SCIENCES↗
NASA NTRS1985

New Techniques for Studying Calcium Gradients

Improved techniques for detecting and manipulating spatial gradients of cytosolic free Ca(2+) concentrations (Ca(2)) sub i and intracellular stores are discussed. Three areas of progress are: (1) development of new fluorescent indicators for Ca(2+) that are the first to be suitable for measuring Ca(2+)) sub i and its inhomogeneities in individual cells; (2) invention of photolabile chelators which shift irreversibly from high to low affinity for Ca(2+) upon illumination, permitting light-controlled jumps in (Ca(2+)) sub i; and (3) fixation methods to trap dynamic intraorganellar Ca stores in a form readily visible by electron microscopy.

Tsien, R. Y.↗
DOE OSTI2020

Redox-Based Electrochemical Affinity Sensor for Detection of Aqueous Pertechnetate Anion

Rapid, selective, in-situ detection of TcO4- in multicomponent matrices consisting of interfering anions such as the ubiquitous NO3- and Cl- or the isostructural and isoelectronic CrO42- is challenging. Present sensors mostly lack the selectivity to exclude these interferences, or the sensitivity to meet the detection limits that are lower than the drinking water standards across the globe. This work presents an affinity based electrochemical sensor for TcO4- detection that relies on selective reductive precipitation of aqueous TcO4- induced by a capture probe immobilized on an electrode platform. This results in a direct decrease of the electron transfer current, the magnitude of the decrease being proportional to the amount of TcO4- added. Using this approach, we were able to achieve a detection limit of 1x10-10 M, which is lower than the drinking water standard of 5.2x10-10 M set by United States Environmental Protection Agency. Our proposed approach also allowed us to detect TcO4- from a multicomponent groundwater sample obtained from a well at the Hanford site in Washington (well 299-W19-36) that also contained NO3- , Cl- and CrO42-, without discernably affecting the detection limits.

Chatterjee, Sayandev↗
DOE OSTI2021

Guest-Host Interactions in Clathrate Hydrates: Benchmark MP2 and CCSD(T)/CBS Binding Energies of CH4, CO2 and H2S in (H2O)20 Cages

We present benchmark binding energies of naturally occurring gas molecules CH4, CO2, and H2S in the small cage, namely the pentagonal dodecahedron (512) (H2O)20, which is one of the constituent cages of the 3 major lattices (structures I, II and H) of clathrate hydrates. These weak interactions require higher levels of electron correlation and converge slowly with increasing basis set to the Complete Basis Set (CBS) limit, necessitating the use of large basis sets up to the augcc- pV5Z and subsequent correction for Basis Set Superposition Error (BSSE). For the host hollow (H2O)20 cages we have identified a most stable isomer with binding energy of -200.8 ± 2.1 kcal/mol at the CCSD(T)/CBS limit (-199.2 ± 0.5 kcal/mol at the MP2/CBS limit). Additionally, we report converged second order Moller-Plesset (MP2) CBS binding energies for the encapsulation of guests in the (H2O)20 cage of -4.3 ± 0.1 for CH4@(H2O)20, -6.6 ± 0.1 for CO2@(H2O)20 and -8.5 ± 0.1 kcal/mol for H2S@(H2O)20, respectively. For CH4@(H2O)20, exhibiting the weakest encapsulation affinity among the three, we report CCSD(T)/aug-cc-pVTZ binding energies and, based on them, a CCSD(T)/CBS estimate of -4.75 ± 0.1 kcal/mol. To the best of our knowledge, the CCSD(T)/aug-cc-pVTZ calculation for CH4@(H2O)20 is the largest one reported to date (168 valence electrons, 1978 basis functions and the correlation of 84 doubly occupied and 1873 virtual orbitals) and required a scalable implementation of the (T) module on 6144 nodes (350208 cores) of the “Cori” supercomputer at the National Energy Research Supercomputing Center (NERSC) for a total execution time of 195 minutes (for the (T) part). These efficient scalable implementations of highly correlated methods offer the capability to obtain long-lasting benchmarks of intermolecular interactions in complex systems. They also provide a path towards parametrizing classical potentials needed to study the dynamical and transport properties in these complex systems as well as assess the accuracy of lower scaling electronic structure methods such as Density Functional Theory (DFT) and MP2 including its spin-biased variants.

Heindel, Joseph↗
DOE OSTI2023

Affinity-matured homotypic interactions induce spectrum of PfCSP structures that influence protection from malaria infection

The generation of high-quality antibody responses to Plasmodium falciparum (Pf) circumsporozoite protein (PfCSP), the primary surface antigen of Pf sporozoites, is paramount to the development of an effective malaria vaccine. Here we present an in-depth structural and functional analysis of a panel of potent antibodies encoded by the immunoglobulin heavy chain variable (IGHV) gene IGHV3-33, which is among the most prevalent and potent antibody families induced in the anti-PfCSP immune response and targets the Asn-Ala-Asn-Pro (NANP) repeat region. Cryo-electron microscopy (cryo-EM) reveals a remarkable spectrum of helical antibody-PfCSP structures stabilized by homotypic interactions between tightly packed fragments antigen binding (Fabs), many of which correlate with somatic hypermutation. We demonstrate a key role of these mutated homotypic contacts for high avidity binding to PfCSP and in protection from Pf malaria infection. Together, these data emphasize the importance of anti-homotypic affinity maturation in the frequent selection of IGHV3–33 antibodies and highlight key features underlying the potent protection of this antibody family.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

2.5 Å-resolution structure of human CDK-activating kinase bound to the clinical inhibitor ICEC0942

The human CDK-activating kinase (CAK), composed of CDK7, cyclin H, and MAT1, is involved in the control of transcription initiation and the cell cycle. Because of these activities, it has been identified as a promising target for cancer chemotherapy. A number of CDK7 inhibitors have entered clinical trials, among them ICEC0942 (also known as CT7001). Structural information can aid in improving the affinity and specificity of such drugs or drug candidates, reducing side effects in patients. Here, we have determined the structure of the human CAK in complex with ICEC0942 at 2.5 Å-resolution using cryogenic electron microscopy. Our structure reveals conformational differences of ICEC0942 compared with previous X-ray crystal structures of the CDK2-bound complex, and highlights the critical ability of cryogenic electron microscopy to resolve structures of drug-bound protein complexes without the need to crystalize the protein target.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Molecular Tuning of Reactivity of Zeolite Protons in HZSM-5

In acidic HZSM-5 zeolite, the reactivity of a methanol molecule interacting with the zeolite proton is amenable to modification via coadsorbing a stochiometric amount of an electron density donor E to form the [(E)(CH 3 OH)(HZ)] complex. The rate of the methanol in this complex undergoing dehydration to dimethyl ether was determined for a series of E with proton affinity (PA) ranging from 659 kJ mol –1 for C 6 F 6 to 825 kJ mol –1 for C 4 H 8 O and was found to follow the expression: Ln(Rate) – Ln(Rate N 2 ) = β(PA – PA N 2 ) γ , where E = N 2 is the reference and β and γ are constants. This trend is probably due to the increased stability of the solvated proton in the [(E)(CH 3 OH)(HZ)] complex with increasing PA. Importantly, this is also observed in steady-state flow reactions when stoichiometric quantities of E are preadsorbed on the zeolite. As demonstrated with E being D 2 O, the effect on methanol reactivity diminishes when E is present in excess of the [(E)(CH 3 OH)(HZ)] complex. It is proposed that the methanol dehydration reaction involves [(E)(CH 3 OH)(CH 3 OH)(HZ)] as the transition state, which is supported by the isotopologue distribution of the initial dimethyl ether formed when a flow of CH 3 OH was passed over ZSM-5 containing one CD 3 OH per zeolite proton. Furthermore, the implication of this on the mechanism of catalytic methanol dehydration on HZSM-5 is discussed.

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

Structural basis of the American mink ACE2 binding by Y453F trimeric spike glycoproteins of SARS‐CoV‐2

Abstract Severe Acute Respiratory Syndrome Coronavirus 2 (SARS‐CoV‐2) enters the host cell by binding to angiotensin‐converting enzyme 2 (ACE2). While evolutionarily conserved, ACE2 receptors differ across various species and differential interactions with Spike (S) glycoproteins of SARS‐CoV‐2 viruses impact species specificity. Reverse zoonoses led to SARS‐CoV‐2 outbreaks on multiple American mink (Mustela vison) farms during the pandemic and gave rise to mink‐associated S substitutions known for transmissibility between mink and zoonotic transmission to humans. In this study, we used bio‐layer interferometry (BLI) to discern the differences in binding affinity between multiple human and mink‐derived S glycoproteins of SARS‐CoV‐2 and their respective ACE2 receptors. Further, we conducted a structural analysis of a mink variant S glycoprotein and American mink ACE2 (mvACE2) using cryo‐electron microscopy (cryo‐EM), revealing four distinct conformations. We discovered a novel intermediary conformation where the mvACE2 receptor is bound to the receptor‐binding domain (RBD) of the S glycoprotein in a “down” position, approximately 34° lower than previously reported “up” RBD. Finally, we compared residue interactions in the S‐ACE2 complex interface of S glycoprotein conformations with varying RBD orientations. These findings provide valuable insights into the molecular mechanisms of SARS‐CoV‐2 entry.

Virology↗
DOE OSTI2020

Spectroscopic evidence for intact carbonic acid stabilized by halide anions in the gas phase

Here we show elusive carbonic acid being effectively stabilized in the gas phase by interacting with halide anions X – (X = F, Cl, Br, and I). The formed H 2 CO 3 ·X – complexes, characterized by negative ion photoelectron spectroscopy and ab initio calculations, all contain intact trans – trans carbonic acid binding onto the respective halide via two identical strong ionic O–H...X – hydrogen bonds. For X = Cl, Br, and I, the complex spectra exhibit the corresponding X – signature by simply shifting to the higher binding energy side, while an extremely 2 eV wide broader band is observed for X = F. This spectroscopic evidence indicates that an excess electron is removed from each halide in the former case, while a proton is transferred from carbonic acid to fluoride upon electron detachment for the latter. The above H 2 CO 3 ·X – structures as well as those of the previously studied H 2 SO 4 ·X – along the homologous halogen series cannot be explained using the proton affinity (PA) argument. Instead, a qualitative correlation is found between these structural motifs and the constituent acid p K a values, strongly suggesting that p K a is a more suitable factor to predict correct acid–base chemistry between these diprotic oxyacids and halides.

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

Organic superbases in Lewis pair catalyzed hydrogenations of imines

Organic superbases have recently emerged as powerful components in metal-free catalytic systems, yet their role in frustrated Lewis pair (FLP) catalyzed hydrogenation reactions remain underexplored. In this article, we investigate the diphosphazene superbases P 2 - t Bu (1) and P 2 -Et (2) as base components combined with electronically tunable boranes of formula 9-(X n -C 6 H 5-n )BBN, where X n = 4-NMe₂, 4-OMe, 4-Me, 4-H, 4-F, 4-OCF 3 , 4-CF 3 , 3,5-(CF3), in FLP-catalyzed hydrogenations of imines. While the more sterically encumbered base 1 forms persistent FLPs whose activity correlates with the hydride affinity of the borane, less hindered base 2 generates Lewis acid–base adducts and displays superior catalytic performance, especially with boranes of lower hydride affinity. A systematic screening identified the adduct 2/9-(4-MeO-C 6 H 4 )BBN as the most active catalytic system, achieving quantitative hydrogenation of N-benzylidene aniline at 80 °C and H 2 pressures as low as 40 bar in THF. Multinuclear NMR spectroscopic studies and DFT calculations support a mechanistic scenario in which reversible adduct formation and subsequent dissociation to the free acid–base pair precede heterolytic H₂ cleavage, with adduct stability and borane electrophilicity concurrently dictating catalytic activity. Under optimized conditions, the most active catalyst system, 2/9-(4-MeO-C 6 H 4 )BBN, hydrogenates a broad range of aldimines, including electron-rich 4-NMe₂ and push-pull substrates, mono- and bis-ortho-substituted imines, and selected heteroaryl imines, with excellent yields and selectivity. Collectively, these findings establish design principles for tuning BBN-derived FLP systems and expand the scope of metal-free hydrogenation catalysis.

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

Confinement-controlled selective CO 2 insertion into a dicopper dihydride core: A multiscale mechanistic study

CO 2 is an abundant C 1 feedstock for fuel and chemical synthesis. We have previously demonstrated experimentally a stepwise insertion of CO 2 into a [Cu 2 H 2 ] core via a solid–gas in crystallo reaction, forming formate species that are unstable and inaccessible under solution-phase conditions. This work elucidates how structural confinement within the crystal lattice enables such selective reactivity. In particular, co-crystallized tetrahydrofuran molecules induce site asymmetry around the [Cu 2 H 2 ] unit, modulating both the local electronic environment and CO 2 diffusion pathways. Using a multiscale computational approach that combines classical molecular mechanics, hybrid quantum mechanics/molecular mechanics molecular dynamics, and enhanced-sampling free energy calculations, we demonstrate how site asymmetry affects CO 2 binding affinities and reaction pathways. These results provide detailed mechanistic insight into CO 2 insertion and hydride transfer, highlighting key differences between crystal- and solution-phase pathways and offering a general framework for understanding how lattice confinement shapes chemical reactivity.

Chemical bonding↗
DOE OSTI2024

Cryo-EM structure of a photosystem I variant containing an unusual plastoquinone derivative in its electron transfer chain

Photosystem I (PS I) is a light-driven oxidoreductase responsible for converting photons into chemical bond energy. Its application for renewable energy was revolutionized by the creation of the MenB deletion (ΔmenB) variant in the cyanobacterium Synechocystis sp. PCC 6803, in which phylloquinone is replaced by plastoquinone-9 with a low binding affinity. This permits its exchange with exogenous quinones covalently coupled to dihydrogen catalysts that bind with high affinity, thereby converting PS I into a stable solar fuel catalyst. Here, we reveal the 2.03-Å-resolution cryo-EM structure of a recent MenB variant of PS I. The quinones and their binding environment are analyzed in the context of previous biophysical data, thereby enabling a protocol to solve future PS I hybrids and constructs from this genetically tractable cyanobacterium.

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

Computing the Relative Affinity of Chlorophylls a and b to Light-Harvesting Complex II

In plants and algae, the primary antenna protein bound to photosystem II is light-harvesting complex II (LHCII), a pigment–protein complex that binds eight chlorophyll (Chl) a molecules and six Chl b molecules. Chl a and Chl b differ only in that Chl a has a methyl group (–CH 3 ) on one of its pyrrole rings, while Chl b has a formyl group (–CHO) at that position. This blue-shifts the Chl b absorbance relative to Chl a . It is not known how the protein selectively binds the right Chl type at each site. Knowing the selection criteria would allow the design of light-harvesting complexes that bind different Chl types, modifying an organism to utilize the light of different wavelengths. The difference in the binding affinity of Chl a and Chl b in pea and spinach LHCII was calculated using multiconformation continuum electrostatics and free energy perturbation. Both methods have identified some Chl sites where the bound Chl type ( a or b ) has a significantly higher affinity, especially when the protein provides a hydrogen bond for the Chl b formyl group. However, the Chl a sites often have little calculated preference for one Chl type, so they are predicted to bind a mixture of Chl a and b . The electron density of the spinach LHCII was reanalyzed, which, however, confirmed that there is negligible Chl b in the Chl a -binding sites. Finally, it is suggested that the protein chooses the correct Chl type during folding, segregating the preferred Chl to the correct binding site.

chemical calculations↗
DOE OSTI2025

Cyclic Peptides for Lanthanide Binding

Lanthanide ions are difficult to separate from one another due to their similar chemical properties. The discovery of lanthanide-binding peptides and proteins in nature has led to an increased interest in the possibility of utilizing the strong binding of peptides to lanthanide ions for their separations; as such, there has been an effort to identify or design peptides with improved lanthanide binding and selectivity toward particular lanthanide ions. Here, in this study, we designed and characterized lanthanide-binding cyclic peptides (LBCPs) with molecular dynamics simulations, electronic structure calculations, and emission spectroscopy. Luminescent decay measurements were done to determine the number of water molecules coordinated to the Eu 3+ ion in Eu-LBCP complexes and compare to the predicted number of water molecules by computation to assess the lanthanide-binding affinity of LBCPs. Measured stability constants show binding of the LBCPs to the Eu 3+ ion with stronger than micromolar affinity. We were able to identify multiple peptides that selectively bind to middle lanthanides. We describe the structural basis of the lanthanide-binding selectivity trend with strongest binding to the middle lanthanides, followed by the heavier lanthanides, and finally to the lighter ions.

ions↗
DOE OSTI2021

Modification of the Coordination Environment of Active Sites on MoC for High-Efficiency CH 4 Production

Modulating the coordination environment of active sites on catalyst surfaces is crucial to developing effective catalysts and controlling catalysis, but it is highly challenging. Guided by our first-principles calculations, we experimentally accomplish the modification of the coordination environment of active sites on MoC nanoparticle surfaces by anchoring pyridinic N atom rings of holey graphene on Mo atoms. The rings produce electrostatic forces that enable the tuning of the Mo sites' affinity to reaction intermediates, which passivates Mo hollow sites, activates Mo top sites and reduces the over-adsorption of OH on the Mo active sites, as predicted by the calculations. The atomic-level modification is well confirmed by atomic-resolution imaging, high-resolution electron tomography, synchrotron soft X-ray spectroscopy and operando electrochemical infrared spectroscopy. Consequently, the Faradaic efficiency for CO 2 reduction to CH 4 is enhanced from 16% to 89%, a record high efficiency so far, in aqueous electrolyte. Meantime, it also exhibits a negligible activity loss over 50 h.

77 NANOSCIENCE AND NANOTECHNOLOGY↗