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DOE OSTI2022

Relation between interfacial shear and friction force in 2D materials

Understanding the interfacial properties between an atomic layer and its substrate is of key interest at both the fundamental and technological levels. From Fermi level pinning to strain engineering and superlubricity, the interaction between a single atomic layer and its substrate governs electronic, mechanical and chemical properties. Here, we measure the hardly accessible interfacial transverse shear modulus of an atomic layer on a substrate. By performing measurements on bulk graphite, and on epitaxial graphene films on SiC with different stacking orders and twisting, as well as in the presence of intercalated hydrogen, we find that the interfacial transverse shear modulus is critically controlled by the stacking order and the atomic layer–substrate interaction. Importantly, we demonstrate that this modulus is a pivotal measurable property to control and predict sliding friction in supported two-dimensional materials. The experiments demonstrate a reciprocal relationship between friction force per unit contact area and interfacial shear modulus. As a result, the same relationship emerges from simulations with simple friction models, where the atomic layer– substrate interaction controls the shear stiffness and therefore the resulting friction dissipation.

36 MATERIALS SCIENCE↗

DOE OSTI2024

Substrate binding plasticity revealed by Cryo-EM structures of SLC26A2

SLC26A2 is a vital solute carrier responsible for transporting essential nutritional ions, including sulfate, within the human body. Pathogenic mutations within SLC26A2 give rise to a spectrum of human diseases, ranging from lethal to mild symptoms. The molecular details regarding the versatile substrate-transporter interactions and the impact of pathogenic mutations on SLC26A2 transporter function remain unclear. Here, using cryo-electron microscopy, we determine three high-resolution structures of SLC26A2 in complexes with different substrates. These structures unveil valuable insights, including the distinct features of the homodimer assembly, the dynamic nature of substrate binding, and the potential ramifications of pathogenic mutations. This structural-functional information regarding SLC26A2 will advance our understanding of cellular sulfate transport mechanisms and provide foundations for future therapeutic development against various human diseases.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Conformational and oligomeric states of SPOP from small-angle X-ray scattering and molecular dynamics simulations

Speckle-type POZ protein (SPOP) is a substrate adaptor in the ubiquitin proteasome system, and plays important roles in cell-cycle control, development, and cancer pathogenesis. SPOP forms linear higher-order oligomers following an isodesmic self-association model. Oligomerization is essential for SPOP’s multivalent interactions with substrates, which facilitate phase separation and localization to biomolecular condensates. Structural characterization of SPOP in its oligomeric state and in solution is, however, challenging due to the inherent conformational and compositional heterogeneity of the oligomeric species. Here, we develop an approach to simultaneously and self-consistently characterize the conformational ensemble and the distribution of oligomeric states of SPOP by combining small-angle X-ray scattering (SAXS) and molecular dynamics (MD) simulations. We build initial conformational ensembles of SPOP oligomers using coarse-grained molecular dynamics simulations, and use a Bayesian/maximum entropy approach to refine the ensembles, along with the distribution of oligomeric states, against a concentration series of SAXS experiments. Our results suggest that SPOP oligomers behave as rigid, helical structures in solution, and that a flexible linker region allows SPOP’s substrate-binding domains to extend away from the core of the oligomers. Additionally, our results are in good agreement with previous characterization of the isodesmic self-association of SPOP. In the future, the approach presented here can be extended to other systems to simultaneously characterize structural heterogeneity and self-assembly.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Mapping Hsp104 interactions using cross‐linking mass spectrometry

Molecular machines from the AAA+ (ATPases Associated with diverse cellular Activity) superfamily of protein disaggregases play important roles in protein folding, disaggregation and DNA processing. Recent cryo-EM structures of AAA+ molecular machines have uncovered nuanced changes in their conformation that underlie their specialized functions. Structural knowledge of these molecular machines in complex with substrates begins to explain their mechanism of activity. Here, we explore how cross-linking mass spectrometry (XL-MS) can be used to interpret changes in conformation induced by ATP in Hsp104 and how a substrate may interact with Hsp104. We applied a panel of cross-linking reagents to produce cross-linking maps of Hsp104 and interpret our data on previously determined X-ray and cryo-EM structures of Hsp104 from a thermophilic yeast, Calcarisporiella thermophila. We developed an analysis pipeline to differentiate between intra-subunit and inter-subunit contacts within the hexameric homo-oligomer. We identify cross-links that break the asymmetry that is present in Hsp104 in an ATP-hydrolysis competent conformation but is absent in an ATP-hydrolysis-defective mutant. Finally, we identify contacts between Hsp104 and a selected protein (proprotein convertase subtilisin/kexin type 9 PCSK9) to reveal contacts on the central channel of Hsp104 across the length of this protein indicating that we might have trapped interactions consistent with its translocation. Our simple and robust XL-MS-based experiments and methods help interpret how these molecular machines change conformation and bind to other proteins even in the context of homo-oligomeric assemblies enabling coupling state-of-the-art modeling approaches with XL-MS.

60 APPLIED LIFE SCIENCES↗

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 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 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 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 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↗

DOE OSTI2023

The Mycobacterium tuberculosis protein O -phosphorylation landscape

Bacterial phosphosignaling has long been synonymous with the histidine kinases of the two component systems (TCSs), but many bacteria, including Mycobacterium tuberculosis (Mtb), also code for Ser/Thr protein kinases (STPKs). STPKs are the main phosphosignaling enzymes in eukaryotes, but the full extent of phosphorylation on protein Ser/Thr and Tyr (O-phosphorylation) in bacteria is unclear. Here, we explored the global signaling capacity of the STPKs in Mtb. We generated a panel of STPK loss- and gain-of-function strains and measured the resulting O-phosphorylation and transcriptional changes. This deep phosphoproteome shows that O-phosphorylation in Mtb is a vastly underexplored protein modification that affects >70% of the proteome. The substrate-kinase interactions of STPKs show an extensive interface with the transcriptional machinery, resulting in STPK regulation of gene expression of over 30% of Mtb genes. Finally, Mtb O-phosphorylation gives rise to an expansive, distributed, and cooperative network of a complexity that has previously only been associated with eukaryotic phosphosignaling networks.

59 BASIC BIOLOGICAL SCIENCES↗