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At least 127 records · Page 7

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DOE OSTI2021

Defective internal allosteric network imparts dysfunctional ATP/substrate-binding cooperativity in oncogenic chimera of protein kinase A

An aberrant fusion of the DNAJB1 and PRKACA genes generates a chimeric protein kinase (PKA-C DNAJB1 ) in which the J-domain of the heat shock protein 40 is fused to the catalytic α subunit of cAMP-dependent protein kinase A (PKA-C). Deceivingly, this chimeric construct appears to be fully functional, as it phosphorylates canonical substrates, forms holoenzymes, responds to cAMP activation, and recognizes the endogenous inhibitor PKI. Nonetheless, PKA-C DNAJB1 has been recognized as the primary driver of fibrolamellar hepatocellular carcinoma and is implicated in other neoplasms for which the molecular mechanisms remain elusive. Here we determined the chimera’s allosteric response to nucleotide and pseudo-substrate binding. We found that the fusion of the dynamic J-domain to PKA-C disrupts the internal allosteric network, causing dramatic attenuation of the nucleotide/PKI binding cooperativity. Our findings suggest that the reduced allosteric cooperativity exhibited by PKA-C DNAJB1 alters specific recognitions and interactions between substrates and regulatory partners contributing to dysregulation.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2018

Crystal structure of the delta-class glutathione transferase in Musca domestica

Highlights: • Delta- and epsilon-class glutathione transferases detoxify insecticides in insects. • Delta-class GST in Musca domestica was crystalized. • Substrate binding pocket of delta-class GST is exposed to solvent and wide open. • C-terminal region of the delta-class GST contributes to catalytic activity. Among the various glutathione transferase (GST) isozymes in insects, the delta- and epsilon-class GSTs fulfill critical functions during the detoxification of insecticides. We crystalized MdGSTD1, the major delta-class GST isozyme in the housefly (Musca domestica), in complex with glutathione (GSH) and solved its structure at a resolution of 1.4 Å. The overall folding of MdGSTD1 resembled other known delta-class GSTs. Its substrate binding pocket was exposed to solvent and considerably more open than in the epsilon-class GST from M. domestica (MdGSTE2). However, their C-terminal structures differed the most because of the different lengths of the C-terminal regions. Although this region does not seem to directly interact with substrates, its deletion reduced the enzymatic activity by more than 70%, indicating a function in maintaining the proper conformation of the binding pocket. Binding of GSH to the GSH-binding region of MdGSTD1 results in a rigid conformation of this region. Although MdGSTD1 has a higher affinity for GSH than the epsilon class enzymes, the thiol group of the GSH molecule was not close enough to serine residue 9 to form a hydrogen-bond with this residue, which is predicted to act as the catalytic center for thiol group deprotonation in GSH.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2023

Influence of Potassium Metal‐Support Interactions on Dendrite Growth

Abstract Combined synchrotron X‐ray nanotomography imaging, cryogenic electron microscopy (cryo‐EM) and modeling elucidate how potassium (K) metal‐support energetics influence electrodeposit microstructure. Three model supports are employed: O‐functionalized carbon cloth (potassiophilic, fully‐wetted), non‐functionalized cloth and Cu foil (potassiophobic, nonwetted). Nanotomography and focused ion beam (cryo‐FIB) cross‐sections yield complementary three‐dimensional (3D) maps of cycled electrodeposits. Electrodeposit on potassiophobic support is a triphasic sponge, with fibrous dendrites covered by solid electrolyte interphase (SEI) and interspersed with nanopores (sub‐10 nm to 100 nm scale). Lage cracks and voids are also a key feature. On potassiophilic support, the deposit is dense and pore‐free, with uniform surface and SEI morphology. Mesoscale modeling captures the critical role of substrate‐metal interaction on K metal film nucleation and growth, as well as the associated stress state.

Liu, Pengcheng↗

DOE OSTI2023

Influence of Potassium Metal-Support Interactions on Dendrite Growth

We report combined synchrotron X-ray nanotomography imaging, cryogenic electron microscopy (cryo-EM) and modeling elucidate how potassium (K) metal-support energetics influence electrodeposit microstructure. Three model supports are employed: O-functionalized carbon cloth (potassiophilic, fully-wetted), non-functionalized cloth and Cu foil (potassiophobic, nonwetted). Nanotomography and focused ion beam (cryo-FIB) cross-sections yield complementary three-dimensional (3D) maps of cycled electrodeposits. Electrodeposit on potassiophobic support is a triphasic sponge, with fibrous dendrites covered by solid electrolyte interphase (SEI) and interspersed with nanopores (sub-10 nm to 100 nm scale). Lage cracks and voids are also a key feature. On potassiophilic support, the deposit is dense and pore-free, with uniform surface and SEI morphology. Mesoscale modeling captures the critical role of substrate-metal interaction on K metal film nucleation and growth, as well as the associated stress state.

36 MATERIALS SCIENCE↗

DOE OSTI2019

Active-Site Druggability of Carbapenemases and Broad-Spectrum Inhibitor Discovery

Serine and metallo-carbapenemases are a serious health concern due to their capability to hydrolyze nearly all β-lactam antibiotics. However, the molecular basis for their unique broad-spectrum substrate profile is poorly understood, particularly for serine carbapenemases, such as KPC-2. Using substrates and newly identified small molecules, we compared the ligand binding properties of KPC-2 with the noncarbapenemase CTX-M-14, both of which are Class A β-lactamases with highly similar active sites. Notably, compared to CTX-M-14, KPC-2 was more potently inhibited by hydrolyzed β-lactam products (product inhibition), as well as by a series of novel tetrazole-based inhibitors selected from molecular docking against CTX-M-14. Together with complex crystal structures, these data suggest that the KPC-2 active site has an enhanced ability to form favorable interactions with substrates and small molecule ligands due to its increased hydrophobicity and flexibility. Such properties are even more pronounced in metallo-carbapenemases, such as NDM-1, which was also inhibited by some of the novel tetrazole compounds, including one displaying comparable low μM affinities against both KPC-2 and NDM-1. Our results suggest that carbapenemase activity confers an evolutionary advantage on producers via a broad β-lactam substrate scope but also a mechanistic Achilles’ heel that can be exploited for new inhibitor discovery. The complex structures show, for the first time, how noncovalent inhibitors can be engineered to simultaneously target both serine and metallo-carbapenemases. Despite the relatively modest activity of the current compounds, these studies also demonstrate that hydrolyzed products and tetrazole-based chemotypes can provide valuable starting points for broad-spectrum inhibitor discovery against carbapenemases.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2018

Concentration Dependence of Dopant Electronic Structure in Bottom-up Graphene Nanoribbons

Bottom-up fabrication techniques enable atomically precise integration of dopant atoms into the structure of graphene nanoribbons (GNRs). Such dopants exhibit perfect alignment within GNRs and behave differently from bulk semiconductor dopants. The effect of dopant concentration on the electronic structure of GNRs, however, remains unclear despite its importance in future electronics applications. Here we use scanning tunneling microscopy and first-principles calculations to investigate the electronic structure of bottom-up synthesized N = 7 armchair GNRs featuring varying concentrations of boron dopants. First-principles calculations of freestanding GNRs predict that the inclusion of boron atoms into a GNR backbone should induce two sharp dopant states whose energy splitting varies with dopant concentration. Scanning tunneling spectroscopy experiments, however, reveal two broad dopant states with an energy splitting greater than expected. Here, this anomalous behavior results from an unusual hybridization between the dopant states and the Au(111) surface, with the dopant–surface interaction strength dictated by the dopant orbital symmetry.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Strongly correlated Chern insulators in magic-angle twisted bilayer graphene

Interactions between electrons and the topology of their energy bands can create unusual quantum phases of matter. Most topological electronic phases appear in systems with weak electron–electron interactions. The instances in which topological phases emerge only as a result of strong interactions are rare and mostly limited to those realized in intense magnetic fields. The discovery of flat electronic bands with topological character in magic-angle twisted bilayer graphene (MATBG) has created a unique opportunity to search for strongly correlated topological phases. Here we introduce a local spectroscopic technique using a scanning tunnelling microscope to detect a sequence of topological insulators in MATBG with Chern numbers C = ±1, ±2 and ±3, which form near filling factors of ±3, ±2 and ±1 electrons per moiré unit cell, respectively, and are stabilized by modest magnetic fields. One of the phases detected here (C = +1) was previously observed when the sublattice symmetry of MATBG was intentionally broken by a hexagonal boron nitride substrate, with interactions having a secondary role. We also demonstrate that strong electron–electron interactions alone can produce not only the previously observed phase, but also other unexpected Chern insulating phases in MATBG. The full sequence of phases that we observe can be understood by postulating that strong correlations favour breaking time-reversal symmetry to form Chern insulators that are stabilized by weak magnetic fields. Our findings illustrate that many-body correlations can create topological phases in moiré systems beyond those anticipated from weakly interacting models.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2019

Determination of the Evolution of Heterogeneous Single Metal Atoms and Nanoclusters under Reaction Conditions: Which Are the Working Catalytic Sites?

Identification of active sites in heterogeneous metal catalysts is critical for understanding the reaction mechanism at the molecular level and for designing more efficient catalysts. Because of their structural flexibility, subnanometric metal catalysts, including single atoms and clusters with a few atoms, can exhibit dynamic structural evolution when interacting with substrate molecules, making it difficult to determine the catalytically active sites. Here, Pt catalysts containing selected types of Pt entities (from single atoms to clusters and nanoparticles) have been prepared, and their evolution has been followed, while they were reacting in a variety of heterogeneous catalytic reactions, including selective hydrogenation reactions, CO oxidation, dehydrogenation of propane, and photocatalytic H2 evolution reaction. By in situ X-ray absorption spectroscopy, in situ IR spectroscopy, and high-resolution electron microscopy techniques, we will show that some characterization techniques carried out in an inadequate way can introduce confusion on the interpretation of coordination environment of highly dispersed Pt species. Finally, the combination of catalytic reactivity and in situ characterization techniques shows that, depending on the catalyst–reactant interaction and metal–support interaction, singly dispersed metal atoms can rapidly evolve into metal clusters or nanoparticles, being the working active sites for those abovementioned heterogeneous reactions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Influence of AA6061 surface preparation on the resistance to surface degradation of thermally grown boehmite films

Understanding substrate–coating interactions is crucial for designing durable, corrosion-resistant systems. This study investigates the effects of surface treatments— polishing, acid etching, and alkaline etching—on AA6061 aluminum alloy and its thermally grown boehmite coatings. Surface treatments were found to significantly alter boehmite film properties by modifying the alloy’s surface composition. X-ray photoelectron spectroscopy revealed a 10% alumina drop after acid etching alongside chemisorbed species formation in wet treatments. Structural analysis, including grazing incidence X-ray diffraction and TEM, showed α-Al 2 O 3 formation on polished surfaces, improving wear resistance but inducing cathodic E corr shifts, pointing to higher corrosion susceptibility. In contrast, acid and alkaline etching produced anodic E corr shifts with stable, pit-free films observed via potentiodynamic scans. Electrochemical impedance spectroscopy highlighted reduced oxide resistance with extended boehmite growth. The findings emphasize the role of surface pre-treatments and boehmite optimization in balancing durability and corrosion resistance for AA6061 substrates.

AA6061↗

DOE OSTI2026

Divergent carbon use efficiency-growth rate tradeoff in popular biological growth models

Carbon use efficiency (CUE) is an important trait emerging from processes regulating biological growth. CUE can be computed either based on the growth of structural biomass or total biomass divided by substrate uptake rate. Nonequilibrium thermodynamics and observations suggest that, for an exponentially growing population of cells, structural biomass CUE should first increase, then peak, and finally decrease with specific growth rate; meanwhile, total biomass CUE increases asymptotically with specific growth rate. We compared predictions from six popular models that are often used for plant and microbial growth in existing ecosystem models. We found that, for an exponentially growing population of biological cells, (1) the source-driven Pirt and Compromise models predict that structural biomass CUE increase asymptotically with growth rate; (2) the apparent sink-driven modified Droop model predicts that structural biomass CUE decreases with growth rate; and (3) the sink-driven variable internal storage model and two dynamic energy budget models predict that structural biomass CUE first increases, then peaks, and finally decreases with growth rate. Moreover, the modified Droop model predicts that total biomass CUE is constant with growth rate, while all other five models predict that total biomass CUE increases with growth rate asymptotically. For non-exponential biological growth, we show that there is no static relationship between total biomass CUE or structural biomass CUE with respect to either growth rate or temperature. Therefore, we contend that biological growth models should explicitly represent interactions between substrate acquisition, substate transformation, and maintenance respiration to better capture observed CUE dynamics, and the sink-driven model should be preferred for general ecosystem biogeochemistry modeling.

Tang, Jinyun [Lawrence Berkeley National Laborator↗

DOE OSTI2023

Intermetallics Based on Sodium Chalcogenides Promote Stable Electrodeposition–Electrodissolution of Sodium Metal Anodes

Sodiophilic micro-composite films of sodium-chalcogenide intermetallics (Na 2 Te and Na 2 S) and Cu particles are fabricated onto commercial copper foam current collectors (Na 2 Te@CF and Na 2 S@CF). For the first time a controllable capacity thermal infusion process is demonstrated. Enhanced wetting by the metal electrodeposition leads to state-of-the-art electrochemical performance. For example, Na 2 Te@CF-based half-cells demonstrate stable cycling at 6 mA cm -2 and 6 mAh cm -2 , corresponding to 54 µm of Na electrodeposited/electrodissolved by geometric area. Sodium metal batteries with Na 3 V 2 (PO 4 ) 3 cathodes are stable at 30C (7 mA cm -2 ) and for 10 000 cycles at 5C and 10C. Cross-sectional cryogenic focused ion beam (cryo-FIB) microscopy details deposited and remnant dissolved microstructures. Sodium metal electrodeposition onto Na 2 Te@CF is dense, smooth, and free of dendrites or pores. On unmodified copper foam, sodium grows in a filament-like manner, not requiring cycling to achieve this geometry. Substrate–metal interaction critically affects the metal–electrolyte interface, namely the thickness and morphology of the solid electrolyte interphase. Density functional theory and mesoscale simulations provide insight into support-adatom energetics, nucleation response, and early-stage morphological evolution. On Na 2 Te sodium atomic dispersion is thermodynamically more stable than isolated clusters, leading to conformal adatom coverage of the surface.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Supramolecular Enhancement of Electrochemical Nitrate Reduction Catalyzed by Cobalt Porphyrin Organic Cages for Ammonia Electrosynthesis in Water**

Abstract The electrochemical nitrate (NO 3 − ) reduction reaction (NO 3 RR) to ammonia (NH 3 ) represents a sustainable approach for denitrification to balance global nitrogen cycles and an alternative to traditional thermal Haber‐Bosch processes. Here, we present a supramolecular strategy for promoting NH 3 production in water from NO 3 RR by integrating two‐dimensional (2D) molecular cobalt porphyrin ( CoTPP ) units into a three‐dimensional (3D) porous organic cage architecture. The porphyrin box CoPB‐C8 enhances electrochemical active site exposure, facilitates substrate–catalyst interactions, and improves catalyst stability, leading to turnover numbers and frequencies for NH 3 production exceeding 200,000 and 56 s −1 , respectively. These values represent a 15‐fold increase in NO 3 RR activity and 200‐mV improvement in overpotential for the 3D CoPB‐C8 box structure compared to its 2D CoTPP counterpart. Synthetic tuning of peripheral alkyl substituents highlights the importance of supramolecular porosity and cavity size on electrochemical NO 3 RR activity. These findings establish the incorporation of 2D molecular units into 3D confined space microenvironments as an effective supramolecular design strategy for enhancing electrocatalysis.

An, Lun↗

DOE OSTI2023

Supramolecular Enhancement of Electrochemical Nitrate Reduction Catalyzed by Cobalt Porphyrin Organic Cages for Ammonia Electrosynthesis in Water**

An, Lun↗

DOE OSTI2019

Experimental Determination of the Sn-Cu-Ni Phase Diagram for Pb-Free Solder Applications

The rapid increase of scrapped electrical products disposed in landfill sites is significantly influencing the environment because of the composition of the associated components. This situation has been the stimulus for the international community to issue a directive to prohibit the use of Pb-containing solders in electronic devices and effectively ban such products on the market. The Sn-Cu-Ni has become increasingly significant as it is used in several solder alloys and more generally both Cu and Ni are common substrates that interact with Sn-based solders in microelectronic applications. However, there is currently an insufficient understanding of the phase equilibria and the associated phase diagrams of many Sn alloys. The present work implemented an experimental methodology to obtain high accuracy results for the phase equilibria between one liquid and one or two intermetallic compounds. The Sn-Cu-Ni and the associated Sn-Cu and Sn-Ni binary systems have been re-evaluated and compared with the literature. The liquidus and the invariant lines were determined for the Sn-Cu-Ni ternary at the temperatures ranges of between 240 °C and 270 °C. The result will contribute to filling phase equilibria data gaps in the Sn-rich corner of the Sn-Cu-Ni alloy system.

36 MATERIALS SCIENCE↗

DOE OSTI2025

Metal–Organic Frameworks as Catalysts for (De)Hydrogenation: Progress, Challenges, and Perspectives

Storing hydrogen through chemical bonding in liquid-organic hydrogen carriers (LOHCs) offers a safer and more practical approach for hydrogen transportation compared to physical liquefaction, which is limited by low volumetric efficiency and gas release. The efficiency of LOHC systems is highly dependent on effective catalysts, which are typically composed of transition metals supported on metal oxides. However, these materials often rely upon costly noble metals, and their nonuniform nature limits mechanistic insights and structure–function relationships that could improve catalyst design. Metal–organic frameworks (MOFs) are promising alternatives to existing catalysts due to their crystalline, tunable, and porous nature. However, their use as catalysts for (de)hydrogenation reactions remains largely underexplored. Related to this, we identify two general classes of MOFs reported as catalysts for (de)hydrogenation reactions: MOFs as scaffolds for catalytically active species and MOFs that function as reactive materials themselves. MOF composites anchor reactive nanoparticles or homogeneous species, imparting reactivity to the framework. The confinement effects experienced by the affixed species, combined with favorable substrate adsorption interactions or acid sites provided by the MOF, enhance the stability, selectivity, and activity of these catalysts for (de)hydrogenation reactions. Additionally, catalytically active MOFs often feature open metal sites at the node or undergo postsynthetic modification at either node or linker to impart reactivity. Here, taking inspiration from these materials, we outline the current state and key challenges of utilizing MOFs as (de)hydrogenation catalysts and propose research pathways to advance materials in this field for energy applications.

Catalysts↗

DOE OSTI2019

Mechanistic Implications of Reductive Co–C Bond Cleavage in B 12 -Dependent Methylmalonyl CoA Mutase

Vitamin B12-dependent enzymes catalyze several difficult radical reactions. However, there are fundamental open questions that need to be addressed to fully understand the formation of highly reactive radical species, its dynamics and interaction with substrate and enzyme. In this work, the possible role of a Proton Coupled Electron Transfer (PCET) pathway concurrent with the Co-C bond activation was investigated. Car-Parrinello molecular dynamics (CPMD) was performed within a QM/MM framework on a reduced AdoCbl cofactor, which was taken as a post-PCET initial step in the activation of the AdoCbl-dependent methylmalonyl CoA mutase (MCM) enzyme. The calculated free energy profile reveals two possible pathways with similar energies, stepwise (I) and concerted (II) for the reductive Co-C cleavage and subsequent H-abstraction. The concerted pathway may be preferred kinetically, because it avoids the formation of a high-energy radical intermediate with possibly a larger recrossing rate. Our results are consistent with the previous proposal of the conductor hypothesis, indicating the explicit role of cob(II)alamin in stabilizing the radical intermediate involved in H-atom transfer.

Vitamin B12, Molecular Dynamics, QM/MM↗

DOE OSTI2025

The Role of Surface Hydroxyls in Dehydration and Dehydrogenation of Formic Acid on Fe 3 O 4 (001)

Understanding the role of surface structure and hydroxylation in catalytic reactions on metal oxide surfaces is important for developing a mechanistic insight into the complex interface processes. Here, we investigate the reactivity of formic acid on reconstructed Fe 3 O 4 (001) using a combination of X-ray photoelectron spectroscopy, infrared reflection absorption spectroscopy, temperature-programmed reaction spectroscopy, low energy electron diffraction, and electronic structure calculations. We find that formic acid initially dissociates at low temperatures (< 80 K) into bidentate formate and a hydroxyl up to an initial dosed coverage of two HCOOH per Fe 3 O 4 (001) unit cell. At higher temperatures (> 450 K), formate largely decomposes along the dehydration pathway, producing CO and H 2 O, with dehydrogenation to CO 2 being a minority side reaction. As a first step, water formation leads to surface oxygen extraction via the Mars-van Krevelen mechanism. Computational studies reveal formate embedded in oxygen vacancies as a key intermediate in the CO formation mechanism. CO formation proceeds via two reaction pathways with desorption that peaks at 530 K on the hydroxyl-rich surface and 560 K on the hydroxyl-deficient surface. Atomic hydrogen coadsorption experiments and ab initio calculations reveal that the presence of surface hydroxyls reduces the CO formation barrier. Furthermore, these results highlight the complex interactions between substrate and intermediate species occurring during reactions on metal oxide surfaces.

Adsorption↗

DOE OSTI2023

Conformational restriction shapes the inhibition of a multidrug efflux adaptor protein

Abstract Membrane efflux pumps play a major role in bacterial multidrug resistance. The tripartite multidrug efflux pump system from Escherichia coli , AcrAB-TolC, is a target for inhibition to lessen resistance development and restore antibiotic efficacy, with homologs in other ESKAPE pathogens. Here, we rationalize a mechanism of inhibition against the periplasmic adaptor protein, AcrA, using a combination of hydrogen/deuterium exchange mass spectrometry, cellular efflux assays, and molecular dynamics simulations. We define the structural dynamics of AcrA and find that an inhibitor can inflict long-range stabilisation across all four of its domains, whereas an interacting efflux substrate has minimal effect. Our results support a model where an inhibitor forms a molecular wedge within a cleft between the lipoyl and αβ barrel domains of AcrA, diminishing its conformational transmission of drug-evoked signals from AcrB to TolC. This work provides molecular insights into multidrug adaptor protein function which could be valuable for developing antimicrobial therapeutics.

59 BASIC BIOLOGICAL SCIENCES↗