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At least 883 records · Page 49
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Pressure tuning of competing interactions on a honeycomb lattice

Exchange interactions are mediated via orbital overlaps across chemical bonds. Thus, modifying the bond angles by physical pressure or strain can tune the relative strength of competing interactions. Here we present a remarkable case of such tuning between the Heisenberg (J) and Kitaev (K) exchange, which respectively establish magnetically ordered and spin liquid phases on a honeycomb lattice. We observe a rapid suppression of the Néel temperature (T N ) with pressure in Ag 3 LiRh 2 O 6 , a spin-1/2 honeycomb lattice with both J and K couplings. Using a combined analysis of x-ray data and first-principles calculations, we find that pressure modifies the bond angles in a way that increases the ∣K/J∣ ratio and thereby suppresses T N . Consistent with this picture, we observe a spontaneous onset of muon spin relaxation (μSR) oscillations below T N at low pressure, whereas in the high pressure phase, oscillations appear only when T < T N /2. Unlike other candidate Kitaev materials, Ag 3 LiRh 2 O 6 is tuned toward a quantum critical point by pressure while avoiding a structural dimerization in the relevant pressure range.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Photolytic activation of Ni (II) X 2 L explains how Ni-mediated cross coupling begins

Nickel photocatalysis has recently become vital to organic synthesis, but how the Ni (II) X 2 L pre-catalyst (X = Cl, Br; L = bidentate ligand) becomes activated to Ni (I) XL has remained puzzling and is typically addressed on a case-by-case basis. Here, we reveal a general mechanism where light induces photolysis of the Ni (II) -X bond, either via direct excitation or triplet energy transfer. Photolysis produces Ni (I) XL and a halogen radical, X*. Subsequent hydrogen atom abstraction, often from the solvent, produces a C(sp 3 ) radical, R*, that recombines with Ni (I) to form organonickel(II) complexes, Ni (II) XRL. Rather than acting as a loss pathway, Ni (II) XRL behaves as a light-activated reservoir of Ni (I) via photolysis of the Ni (II) -C bond. These results explain the role of the solvent in protecting the catalyst from off-cycle dimerization, demonstrate that two photons are often required to drive the reaction, and show how tuning the ligand can control the concentration of active Ni (I) species.

08 HYDROGEN↗
DOE OSTI2025

Extending quantum-mechanical benchmark accuracy to biological ligand-pocket interactions

Predicting the binding affinity of ligands to protein pockets is key in the drug design pipeline. The flexibility of ligand-pocket motifs arises from a range of attractive and repulsive electronic interactions during binding. Accurately accounting for all interactions requires robust quantum-mechanical (QM) benchmarks, which are scarce for ligand-pocket systems. Additionally, disagreement between “gold standard” Coupled Cluster (CC) and Quantum Monte Carlo (QMC) methods casts doubt on many benchmarks for larger non-covalent systems. We introduce the “QUantum Interacting Dimer” (QUID) benchmark framework containing 170 non-covalent (non-)equilibrium systems modeling chemically and structurally diverse ligand-pocket motifs. Symmetry-adapted perturbation theory shows that QUID broadly covers non-covalent binding motifs and energetic contributions. Robust binding energies are obtained using complementary CC and QMC methods, achieving agreement of 0.5 kcal/mol. The benchmark data analysis reveals that several dispersion-inclusive density functional approximations provide accurate energy predictions, though their atomic van der Waals forces differ in magnitude and orientation. Contrarily, semiempirical methods and empirical force fields require improvements in capturing non-covalent interactions (NCIs) for out-of-equilibrium geometries. The wide span of NCIs, highly accurate interaction energies, and analysis of molecular properties take QUID beyond the “gold standard” for QM benchmarks of ligand-protein systems.

Puleva, Mirela [University of Luxembourg, Luxembou↗
DOE OSTI2026

Insights into the mechanisms of NH3 inhibition on Cu-CHA SCR catalysts

This work elucidates the atomic-scale mechanism behind ammonia (NH3) inhibition during the selective catalytic reduction (SCR) of NO? on Cu-CHA catalysts, a key issue limiting low-temperature emission control. Using SCR kinetic analysis, operando electron paramagnetic resonance (EPR) spectroscopy, and density functional theory (DFT), we demonstrate that NH3 inhibition primarily slows the oxidation half-cycle (OHC), while the reduction half-cycle (RHC) remains unaffected. DFT simulations reveal that excess NH3 substantially increases the diffusion barrier for CuI ions, hindering formation of essential CuII-oxo dimer intermediates and thus suppressing OHC kinetics. Operando EPR studies confirm that this inhibition strongly depends on operating temperature and catalyst Cu loading. Our findings highlight strategies to counteract NH3 inhibition, including optimizing Cu loading, precisely managing NH3:NO feed ratios, and enhancing CuI ion mobility through tailored catalyst design and operational adjustments, thereby advancing the efficiency of emission control technologies in automotive applications.

Deka, Dhruba Jyoti↗
DOE OSTI2026

Revealing ultrafast proton-transfer-mediated autoionization as a source of low-energy electrons in hydrogen-bonded systems

Ionizing radiation can trigger ultrafast proton transfer, a central mechanism in many chemical and biological functions, that in turn can enable or suppress electron relaxation processes and consequently cause abrupt changes in the reaction pathway. This study combines theory and experiment to probe ultrafast relaxation and dissociation in water dimers following inner- and outer-valence photoionization. By tracking electron and nuclear motion simultaneously, we reveal competing fragmentation pathways that produce low-energy electrons, which are key agents in radiation-induced chemistry, including DNA damage. While low-energy electrons are known to arise via intermolecular Coulombic decay, here we identify a faster relaxation mechanism gated by proton transfer following inner-valence ionization, which we call proton-transfer-mediated autoionization. Occurring within 10 femtoseconds, this process alters fragmentation outcomes, yielding either D 3 O + + OD + or D 2 O + + D 2 O + , depending on the interplay of proton migration and hydrogen back-transfer. Our findings underscore the intricate coupling between electronic and nuclear dynamics in hydrogen-bonded systems and establish proton-transfer-mediated autoionization as a significant pathway for low-energy electron generation.

Atomic and molecular interactions with photons↗
DOE OSTI2023

Structural and biochemical insight into a modular β-1,4-galactan synthase in plants

Rhamnogalacturonan I (RGI) is a structurally complex pectic polysaccharide with a backbone of alternating rhamnose and galacturonic acid residues substituted with arabinan and galactan side chains. Galactan synthase 1 (GalS1) transfers galactose and arabinose to either extend or cap the ..beta..-1,4-galactan side chains of RGI, respectively. Here we report the structure of GalS1 from Populus trichocarpa, showing a modular protein consisting of an N-terminal domain that represents the founding member of a new family of carbohydrate-binding module, CBM95, and a C-terminal glycosyltransferase family 92 (GT92) catalytic domain that adopts a GT-A fold. GalS1 exists as a dimer in vitro, with stem domains interacting across the chains in a 'handshake' orientation that is essential for maintaining stability and activity. In addition to understanding the enzymatic mechanism of GalS1, here we gained insight into the donor and acceptor substrate binding sites using deep evolutionary analysis, molecular simulations and biochemical studies. Combining all the results, a mechanism for GalS1 catalysis and a new model for pectic galactan side-chain addition are proposed.

09 BIOMASS FUELS↗
DOE OSTI2021

Ferromagnetism out of charge fluctuation of strongly correlated electrons in κ -(BEDT-TTF) 2 Hg(SCN) 2 Br

We perform magnetic susceptibility and magnetic torque measurements on the organic κ-(BEDT-TTF) 2 Hg(SCN) 2 Br, which is recently suggested to host an exotic quantum dipole-liquid in its low-temperature insulating phase. Below the metal-insulator (MI) transition temperature, the magnetic susceptibility follows a Curie–Weiss law with a positive Curie–Weiss temperature, and a particular M∝ $\sqrt{H}$ curve is observed. The emergent ferromagnetically interacting spins amount to about 1/6 of the full spin moment of localized charges. Taking account of the possible inhomogeneous quasi-charge-order that forms a dipole-liquid, we construct a model of antiferromagnetically interacting spin chains in two adjacent charge-ordered domains, which are coupled via fluctuating charges on a Mott-dimer at the boundary. We find that the charge fluctuations can draw a weak ferromagnetic moment out of the spin singlet domains.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Understanding temperature-dependent SU(3) spin dynamics in the S = 1 antiferromagnet Ba 2 FeSi 2 O 7

Quantum magnets admit more than one classical limit and N-level systems with strong single-ion anisotropy are expected to be described by a classical approximation based on SU(N) coherent states. Here we test this hypothesis by modeling finite temperature inelastic neutron scattering (INS) data of the effective spin-one antiferromagnet Ba 2 FeSi 2 O 7 . The measured dynamic structure factor is calculated with a generalized Landau-Lifshitz dynamics for SU(3) spins. Unlike the traditional classical limit based on SU(2) coherent states, the results obtained with classical SU(3) spins are in good agreement with the measured temperature dependent spectrum. The SU(3) approach developed here provides a general framework to understand the broad class of materials comprising weakly coupled antiferromagnetic dimers, trimers, or tetramers, and magnets with strong single-ion anisotropy.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Triple tandem trimer immunogens for HIV-1 and influenza nucleic acid-based vaccines

Recombinant native-like HIV-1 envelope glycoprotein (Env) trimers are used in candidate vaccines aimed at inducing broadly neutralizing antibodies. While state-of-the-art SOSIP or single-chain Env designs can be expressed as native-like trimers, undesired monomers, dimers and malformed trimers that elicit non-neutralizing antibodies are also formed, implying that these designs could benefit from further modifications for gene-based vaccination approaches. Here, we describe the triple tandem trimer (TTT) design, in which three Env protomers are genetically linked in a single open reading frame and express as native-like trimers. Viral vectored Env TTT induced similar neutralization titers but with a higher proportion of trimer-specific responses. The TTT design was also applied to generate influenza hemagglutinin (HA) trimers without the need for trimerization domains. Additionally, we used TTT to generate well-folded chimeric Env and HA trimers that harbor protomers from three different strains. In summary, the TTT design is a useful platform for the design of HIV-1 Env and influenza HA immunogens for a multitude of vaccination strategies.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

In situ electrochemical recomposition of decomposed redox-active species in aqueous organic flow batteries

Aqueous organic redox flow batteries (AORFBs) offer a safe and potentially inexpensive solution to the problem of storing massive amounts of electricity produced from intermittent renewables. However, molecular decomposition is the major barrier preventing AORFBs from being commercialized. Structural modifications can improve molecular stability at the expense of increased synthetic cost and molecular weight. Utilizing 2,6-dihydroxy-anthraquinone (DHAQ), without further structural modification, we demonstrate that electrochemical regeneration could be a viable route to achieve low-cost, long-lifetime AORFBs. In situ (online) NMR and EPR and complementary electrochemical analyses reveal that decomposition compounds i.e., 2,6-dihydroxy-anthrone (DHA) and its tautomer, 2,6-dihydroxy-anthranol (DHAL), can be converted back to DHAQ in two steps: first DHA(L) 2- are oxidized to the dimer (DHA) 2 4- at - 0.32 V vs. SHE by one-electron transfer; subsequently, the (DHA) 2 4- is oxidized to DHAQ 2- at +0.57 V vs. SHE by three-electron transfer. Electrochemical regeneration rejuvenates not only DHAQ 2- , but also the positive electrolyte – rebalancing the states of charge of both electrolytes without introducing extra ions. We demonstrate the repeated capacity recovery with DHAQ | potassium ferro-/ferricyanide flow battery in basic conditions, and show the approach is also effective for anthraquinone-2,7-disulfonate in acid. Electrochemical regeneration strategies may extend the useful lifetime of many water-soluble organic molecules with anthraquinone core structures in electrochemical cells.

25 ENERGY STORAGE↗
DOE OSTI2024

Coherent photoexcitation of entangled triplet pair states

The functional properties of organic semiconductors are defined by the interplay between optically bright and dark states. Organic devices require rapid conversion between these bright and dark manifolds for maximum efficiency, and one way to achieve this is through multiexciton generation (S 1 → 1 TT). Here, the dark state 1 TT is typically generated from bright S 1 after optical excitation; however, the mechanistic details are hotly debated. Here we report a 1 TT generation pathway in which it can be coherently photoexcited, without any involvement of bright S 1 . Using <10-fs transient absorption spectroscopy and pumping sub-resonantly, 1 TT is directly generated from the ground state. Applying this method to a range of pentacene dimers and thin films of various aggregation types, we determine the critical material properties that enable this forbidden pathway. Through a strikingly simple technique, this result opens the door for new mechanistic insights into 1 TT and other dark states in organic materials.

14 SOLAR ENERGY↗
DOE OSTI2025

A formal Fe III/V redox couple in an intercalation electrode

Iron redox cycling between low-valent oxidation states of Fe II and Fe III drives crucial processes in nature. The Fe II/III redox couple charge compensates the cycling of lithium iron phosphate, a positive electrode (cathode) for lithium-ion batteries. High-valent iron redox couples, involving formal oxidation higher than Fe III , could deliver higher electrochemical potentials and energy densities. However, because of the instability of high-valent Fe electrodes, they have proven difficult to probe and exploit in intercalation systems. Here, in this study, we report and characterize a formal Fe III/V redox couple by revisiting the charge compensation mechanism of (de)lithiation in Li 4 FeSbO 6 . Valence-sensitive experimental and computational core-level spectroscopy reveal a direct transition from Fe III (3d 5 ) to a negative-charge-transfer FeV (3d 5 L 2 ) ground state on delithiation, without forming Fe IV , or oxygen dimers. We identify that the cation ordering in Li 4 FeSbO 6 drives a templated phase transition to stabilize the unique Fe V species and demonstrate that disrupting cation ordering suppresses the Fe III/V redox couple. Exhibiting resistance to calendar aging, high operating potential and low voltage hysteresis, the Fe III/V redox couple in Li 4 FeSbO 6 provides a framework for developing sustainable, Fe-based intercalation cathodes for high-voltage applications.

Ramachandran, Hari [Stanford Univ., CA (United Sta↗
DOE OSTI2024

Surface-Defect-Passivation-Enabled Near-Unity Charge Collection Efficiency in Bromide-Based Perovskite Gamma-Ray Spectrum Devices

Hybrid lead halide perovskites have superior charge transport properties to all-inorganic perovskites, but high-resolution spectroscopic radiation detectors have not been realized. Here we show that surface deep traps severely limit charge collection in formamidinium lead bromide (FAPbBr3) single-crystal devices, despite having a good bulk transport property. Three types of defect on the crystal surface, namely, FA vacancies, uncoordinated lead and Pb-Pb dimers caused by bromide loss, are found to form deep traps, resulting in non-radiative charge recombinations at the metal/perovskite interface. By tailoring the passivation functional groups, we find that ammonium bromide can passivate all these three deep traps on FAPbBr3 surfaces, improving the charge collection efficiency to near unity. The comparable bulk and surface recombination lifetimes indicate that all the surface defects are effectively passivated. Surface passivation also reduces the dark current by 10 times and decreases the dark counts by ~60 times. The energy resolution of the 137Cs spectra acquired using the FAPbBr3 detectors is improved from 5.7% to 1.7% when all the surface defects are passivated without changing the bulk properties, which is the best among solution-grown semiconductor detectors. Surface passivation is stable for more than six months, and FAPbBr3 spectroscopic detectors can operate at unprecedented high temperatures of more than 130 degrees C.

gamma ray↗
DOE OSTI2020

Structural basis of the activation of a metabotropic GABA receptor

Metabotropic γ-aminobutyric acid receptors (GABA B ) are involved in the modulation of synaptic responses in the central nervous system and have been implicated in neuropsychological conditions that range from addiction to psychosis. GABA B belongs to class C of the G-protein-coupled receptors, and its functional entity comprises an obligate heterodimer that is composed of the GB1 and GB2 subunits. Each subunit possesses an extracellular Venus flytrap domain, which is connected to a canonical seven-transmembrane domain. In this paper we present four cryo-electron microscopy structures of the human full-length GB1–GB2 heterodimer: one structure of its inactive apo state, two intermediate agonist-bound forms and an active form in which the heterodimer is bound to an agonist and a positive allosteric modulator. The structures reveal substantial differences, which shed light on the complex motions that underlie the unique activation mechanism of GABA B . Our results show that agonist binding leads to the closure of the Venus flytrap domain of GB1, triggering a series of transitions, first rearranging and bringing the two transmembrane domains into close contact along transmembrane helix 6 and ultimately inducing conformational rearrangements in the GB2 transmembrane domain via a lever-like mechanism to initiate downstream signalling. This active state is stabilized by a positive allosteric modulator binding at the transmembrane dimerization interface.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Structures of a phycobilisome in light-harvesting and photoprotected states

Phycobilisome (PBS) structures are elaborate antennae in cyanobacteria and red algae 1,2 . These large protein complexes capture incident sunlight and transfer the energy through a network of embedded pigment molecules called bilins to the photosynthetic reaction centres. However, light harvesting must also be balanced against the risks of photodamage. A known mode of photoprotection is mediated by orange carotenoid protein (OCP), which binds to PBS when light intensities are high to mediate photoprotective, non-photochemical quenching 3-6 . Here we use cryogenic electron microscopy to solve four structures of the 6.2 MDa PBS, with and without OCP bound, from the model cyanobacterium Synechocystis sp. PCC 6803. The structures contain a previously undescribed linker protein that binds to the membrane-facing side of PBS. For the unquenched PBS, the structures also reveal three different conformational states of the antenna, two previously unknown. The conformational states result from positional switching of two of the rods and may constitute a new mode of regulation of light harvesting. Further, only one of the three PBS conformations can bind to OCP, which suggests that not every PBS is equally susceptible to non-photochemical quenching. In the OCP-PBS complex, quenching is achieved through the binding of four 34kDa OCPs organized as two dimers. The complex reveals the structure of the active form of OCP, in which an approximately 60Å displacement of its regulatory carboxy terminal domain occurs. Finally, by combining our structure with spectroscopic properties 7 , we elucidate energy transfer pathways within PBS in both the quenched and light-harvesting states. Collectively, our results provide detailed insights into the biophysical underpinnings of the control of cyanobacterial light harvesting. The data also have implications for bioengineering PBS regulation in natural and artificial light-harvesting systems.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Structural basis of broad-spectrum β-lactam resistance in Staphylococcus aureus

Abstract Broad-spectrum β-lactam antibiotic resistance in Staphylococcus aureus is a global healthcare burden 1,2 . In clinical strains, resistance is largely controlled by BlaR1 3 , a receptor that senses β-lactams through the acylation of its sensor domain, inducing transmembrane signalling and activation of the cytoplasmic-facing metalloprotease domain 4 . The metalloprotease domain has a role in BlaI derepression, inducing blaZ (β-lactamase PC1) and mecA (β-lactam-resistant cell-wall transpeptidase PBP2a) expression 3–7 . Here, overcoming hurdles in isolation, we show that BlaR1 cleaves BlaI directly, as necessary for inactivation, with no requirement for additional components as suggested previously 8 . Cryo-electron microscopy structures of BlaR1—the wild type and an autocleavage-deficient F284A mutant, with or without β-lactam—reveal a domain-swapped dimer that we suggest is critical to the stabilization of the signalling loops within. BlaR1 undergoes spontaneous autocleavage in cis between Ser283 and Phe284 and we describe the catalytic mechanism and specificity underlying the self and BlaI cleavage. The structures suggest that allosteric signalling emanates from β-lactam-induced exclusion of the prominent extracellular loop bound competitively in the sensor-domain active site, driving subsequent dynamic motions, including a shift in the sensor towards the membrane and accompanying changes in the zinc metalloprotease domain. We propose that this enhances the expulsion of autocleaved products from the active site, shifting the equilibrium to a state that is permissive of efficient BlaI cleavage. Collectively, this study provides a structure of a two-component signalling receptor that mediates action—in this case, antibiotic resistance—through the direct cleavage of a repressor.

Science & Technology - Other Topics↗
DOE OSTI2023

Structural basis of Gabija anti-phage defence and viral immune evasion

Bacteria encode hundreds of diverse defence systems that protect them from viral infection and inhibit phage propagation. Gabija is one of the most prevalent anti-phage defence systems, occurring in more than 15% of all sequenced bacterial and archaeal genomes, but the molecular basis of how Gabija defends cells from viral infection remains poorly understood. Here we use X-ray crystallography and cryo-electron microscopy (cryo-EM) to define how Gabija proteins assemble into a supramolecular complex of around 500 kDa that degrades phage DNA. Gabija protein A (GajA) is a DNA endonuclease that tetramerizes to form the core of the anti-phage defence complex. Two sets of Gabija protein B (GajB) dimers dock at opposite sides of the complex and create a 4:4 GajA–GajB assembly (hereafter, GajAB) that is essential for phage resistance in vivo. We show that a phage-encoded protein, Gabija anti-defence 1 (Gad1), directly binds to the Gabija GajAB complex and inactivates defence. A cryo-EM structure of the virally inhibited state shows that Gad1 forms an octameric web that encases the GajAB complex and inhibits DNA recognition and cleavage. Our results reveal the structural basis of assembly of the Gabija anti-phage defence complex and define a unique mechanism of viral immune evasion.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

The CRISPR effector Cam1 mediates membrane depolarization for phage defence

Prokaryotic type III CRISPR–Cas systems provide immunity against viruses and plasmids using CRISPR-associated Rossman fold (CARF) protein effectors. Recognition of transcripts of these invaders with sequences that are complementary to CRISPR RNA guides leads to the production of cyclic oligoadenylate second messengers, which bind CARF domains and trigger the activity of an effector domain. Whereas most effectors degrade host and invader nucleic acids, some are predicted to contain transmembrane helices without an enzymatic function. Whether and how these CARF–transmembrane helix fusion proteins facilitate the type III CRISPR–Cas immune response remains unknown. Here we investigate the role of cyclic oligoadenylate-activated membrane protein 1 (Cam1) during type III CRISPR immunity. Structural and biochemical analyses reveal that the CARF domains of a Cam1 dimer bind cyclic tetra-adenylate second messengers. In vivo, Cam1 localizes to the membrane, is predicted to form a tetrameric transmembrane pore, and provides defence against viral infection through the induction of membrane depolarization and growth arrest. These results reveal that CRISPR immunity does not always operate through the degradation of nucleic acids, but is instead mediated via a wider range of cellular responses.

59 BASIC BIOLOGICAL SCIENCES↗