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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 1,315 records · Page 73
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Simultaneous bright- and dark-field X-ray microscopy at X-ray free electron lasers

Abstract The structures, strain fields, and defect distributions in solid materials underlie the mechanical and physical properties across numerous applications. Many modern microstructural microscopy tools characterize crystal grains, domains and defects required to map lattice distortions or deformation, but are limited to studies of the (near) surface. Generally speaking, such tools cannot probe the structural dynamics in a way that is representative of bulk behavior. Synchrotron X-ray diffraction based imaging has long mapped the deeply embedded structural elements, and with enhanced resolution, dark field X-ray microscopy (DFXM) can now map those features with the requisite nm-resolution. However, these techniques still suffer from the required integration times due to limitations from the source and optics. This work extends DFXM to X-ray free electron lasers, showing how the $$10^{12}$$ 10 12 photons per pulse available at these sources offer structural characterization down to 100 fs resolution (orders of magnitude faster than current synchrotron images). We introduce the XFEL DFXM setup with simultaneous bright field microscopy to probe density changes within the same volume. This work presents a comprehensive guide to the multi-modal ultrafast high-resolution X-ray microscope that we constructed and tested at two XFELs, and shows initial data demonstrating two timing strategies to study associated reversible or irreversible lattice dynamics.

47 OTHER INSTRUMENTATION↗
DOE OSTI2022

The weathered bedrock vadose zone: A hidden control on water availability in the western United States (Final Technical Report)

This report summarizes the research completed during the project entitled "The weathered bedrock vadose zone: A hidden control on water availability in the western United States" (Award: DE-SC0018039). The report covers work completed between 9/15/17 and 9/14/20. The objective of the exploratory project work was to evaluate the overarching hypothesis that the subsurface underlying actively eroding landscapes is systematically structured as a result of a balance between weathering and erosion and that this structure leads to dynamic moisture storage within weathered rock. To accomplish project objectives, we characterized hillslope weathering profile structure and conducted subsurface moisture monitoring across four study sites with comparable bedrock types but differing erosion rate and hydroclimate: The Angelo Coast Range Reserve (ACRR), Sagehorn-Russell Ranch (SRR), Antelope Valley Ranch (AVR), and the LBNL Watershed Function Scientific Focus Area (SFA). New characterization and monitoring infrastructure at the AVR and SFA sites was established through this project and enables long-term monitoring of hydrologic and carbon fluxes at the sites for comparison with long-term monitoring in other sites. Deep drilling, downhole logging, and characterization of chemistry and porosity of rock recovered from drilling reveals two weathering fronts across the sites. A shallower front is marked by the extent of pervasive fracturing and oxidation of pyrite and organic carbon. A deeper weathering front is marked by the appearance of open fractures and discoloration. At the AVR site, multiple ridge tops of different hillslope length were investigated to establish the relationship between the weathering front and topography. Drilling reveals that the fraction of the hillslope relief that is weathered scales with hillslope length, consistent with the theoretical framework that guided the project relating groundwater drainage with landscape evolution. With the establishment of new boreholes, we have documented significant water storage in weathered bedrock using low-field borehole nuclear magnetic resonance (NMR) across all four sites. In the upper 4 m of bedrock, the average water contents at ACRR, AVR, SRR, and SFA are approximately 25%, 16%, 25%, 23% respectively. At the ACRR site, where long-term monitoring via neutron probe surveys and time-domain transmission sensors are available, we have demonstrated that NMR reliably records moisture content and importantly, moisture content dynamics in weathered bedrock. Across all sites, our NMR monitoring has also revealed that a considerable fraction of the water storage occurs in fractures or pores that are significantly larger than the fine-grained bedrock matrix of the parent rock. To identify the proportion of water storage occurring in fractures and large pores, we analyzed the NMR signal by evaluating both the sum of echoes and an inversion of the NMR signal for a distribution of T2 relaxation times. Both methods reveal that at least 20% of the water storage occurs in fractures and larger pores across all sites. To constrain the interpretation of the in-situ field-scale NMR measurements, we compare the NMR response in the field to independent pore-structure information obtained via helium pycnometry. Results support the inference that dynamic seasonal water storage is dominantly restricted to the fracture network, which can reach 7% of the total volume. This dynamic range in water content is comparable to that of some soils, underscoring the need to understand how this region of the Earth System is structured, and functions as a hydrologic reservoir.

58 GEOSCIENCES↗
DOE OSTI2021

Thermodynamic properties of Gd-Bi alloys determined by emf measurements in LiCl-KCl-GdCl 3 electrolyte

Thermodynamic properties of binary Gd-Bi alloys (mole fraction, x Gd = 0.02–0.35) were determined using electromotive force (emf) measurements in molten LiCl-KCl-GdCl 3 electrolyte in complement with structural, microstructural, and thermal characterization. X-ray diffractometry (XRD) and scanning electron microscopy (SEM) identified the phase constituents of Gd-Bi alloys (x Gd = 0.02–0.35) as Bi matrix and GdBi compound. According to differential scanning calorimetry (DSC) measurements up to 1250 K, a eutectic transition [L = Bi + GdBi] was observed at 543 K but the reported peritectic transition [L + GdBi = GdBi 2 ] was not detected, suggesting the absence of the GdBi 2 compound. Based on structural, microstructural, and thermal characterization of Gd-Bi alloys (x Gd = 0.02–0.35), the GdBi 2 compound was not detected, and its thermodynamic stability is questionable. The emf of Gd-Bi alloy (x Gd = 0.16) at 700–1048 K relative to Gd(s) was measured by electrodepositing pure Gd metal at 25 K increments. Further, the emf values of Gd-Bi alloys were determined via coulometric titration of Gd into liquid Bi using a two-phase [L + GdBi] alloy as a reference electrode at 773–973 K. The solubility of Gd in liquid Bi was also estimated to be 0.50 mol% (773 K), 0.99 mol% (873 K), and 2.21 mol% (973 K) and the excess partial molar Gibbs energy (Δ$\mathrm{\bar{G}^{ex}_{Gd}}$) of liquid Gd-Bi alloys was as low as 65 kJ mol –1 , indicating strong chemical interactions between Gd and Bi.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Small-Angle X-ray Scattering Analysis of Colloidal Crystals and Replica Materials Made from L-Arginine-Stabilized Silica Nanoparticles

Colloidal crystals made from sub-100 nm silica nanoparticles have provided a versatile platform for the template-assisted synthesis of three-dimensionally interconnected semiconducting, metallic, and magnetic replicas. However, the detailed structure of these materials has not yet been characterized. Here, we investigated the structures of colloidal crystalline films and germanium replicas by scanning electron microscopy and small angle X-ray scattering. The structures of colloidal crystals made by evaporative assembly depends on the size of L-arginine-capped silica nanoparticles. Particles smaller than ~31 nm diameter assemble into non-close-packed arrangements (bcc) whereas particles larger than 31 nm assemble into random close-packed structures with disordered hexagonal phase. Polycrystalline films of these materials retain their structures and long-range order upon infiltration at high temperature and pressure, and the structure is preserved in Ge replicas. The shear force during deposition and dispersity of silica nanoparticles contributes to the size-based variation in the structure and to the size of crystal domains in the colloidal crystal films.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Revealing the Configuration and Conformation of Surface Organometallic Catalysts with DNP-Enhanced NMR

Although single-site, supported organometallic catalysts were designed with homogeneity in mind, little is strictly known about their atomic-level structure and uniformity. This is in large part due to the inability of conventional characterization tools to provide structural information with adequate resolution and range for this purpose. In this work, we show that dynamic nuclear polarization (DNP)-enhanced solid-state nuclear magnetic resonance (NMR) enables the measurement of distances between the surface and individual carbons, making it possible to orient complexes and molecules on surfaces. We use this approach to determine the orientation and configuration of naturally 13 C-abundant acetate and supported organoiridium(III) pincer complex, both supported on γ-Al 2 O 3 . By combining solid-state NMR and extended X-ray absorption fine structure spectroscopy (EXAFS) experiments with periodic density functional theory (DFT) calculations, we are able to determine the three-dimensional arrangement of ligands around the metal center and thereby identify the structure of the supported complex at a resolution reminiscent of that associated with single-crystal diffractometry.

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

Second Annual Progress Report on Correlation Between Microstructure and Mechanical Properties of Neutron-Irradiated Ferritic-Martensitic and Austenitic Steels

Ferritic-martensitic steels G92-2b (an optimized Grade 92 heat), NF616 and T91, and austenitic stainless steel 800H and its Grain Boundary Engineering (GBE)-treated version 800H-TMP (ThermoMechanical Processing) were irradiated in the High Flux Isotope Reactor (HFIR) of Oak Ridge National Laboratory (ORNL) and the Advanced Test Reactor (ATR) of Idaho National Laboratory (INL). Selected G92-2b samples were irradiated up to 14.66 dpa in the HFIR at two temperature ranges: 400–496.7°C and 683.3– 720°C. NF616 and T91 were irradiated in the ATR up to 8.16 dpa with the irradiation temperatures ranged from 241°C to 447.5°C. Alloy 800H and 800H-TMP samples were irradiated in both the HFIR and the ATR. Selected 800H and 800H-TMP samples had HFIR irradiation to 1.28 dpa at 580°C and ATR irradiation up to 9.12 dpa at 359°C to 431°C. Vickers hardness measurements, fractography, and microstructural characterization were performed on the selected samples in the Low Activation Materials Design and Analysis (LAMDA) laboratory. Radiation-hardening of G92-2b was observed at the lower doses and lower irradiation temperatures (400- 496.7°C), with GB03 (0.52 dpa at 400°C) and GB04 (7.44 dpa at ~490°C) showing ~12% and ~8% hardening, respectively. Softening by ~14% was observed for GB05 (14.66 dpa at 496.7°C). Radiationsoftening of G92-2b was more prevalent at the higher irradiation temperatures (683.3-~720°C), with GB10 (0.46 dpa at 683.3°C), GB11 (7.44 dpa at ~720°C), and GB12 (14.63 dpa at ~720°C) showing ~8%, ~8%, and ~40% softening, respectively. Radiation-hardening of NF616 and T91 was observed with the hardness increased by ~37% to ~65% depending on the irradiation doses and irradiation temperatures. Within the studied irradiation conditions of NF616 and T91, samples with a higher dose had a larger hardness after irradiation. All the tested alloy 800H and 800H-TMP samples in this work showed radiation-hardening by ~96±7% to ~152±10%. Alloy 800H-TMP tended to have slightly smaller radiation-hardening than alloy 800H. The fractography results of G92-2b sample GB03, GB10, and GB11, together with the previously characterized fractography of GB04, GB05, and GB12, indicated that the ductility of G92-2b was maintained up to 14.66 dpa at the lower irradiation temperatures of 400-496.7°C, while some loss of ductility (less necking) was observed for higher doses at the higher irradiation temperatures of 683.3-720°C. This agrees with the previously reported tensile test results of G92-2b, where the elongation of G92-2b was reduced at higher doses at the higher irradiation temperatures. Dimple sizes increased at higher doses, which are more evident at the higher irradiation temperatures of 683.3-~720°C. The fractography of NF616 sample D2 (2.96 dpa at 291.5°C), D4 (5.91 dpa at 359°C), and D6 (8.16 dpa at 431°C) indicated loss of ductility with negligible necking for sample D2, while ductile failure for samples D4 and D6. Fractography of alloy 800H and 800H-TMP samples in various irradiation conditions showed ductile failure with obvious necking. Dimples were observed, with some of them containing large Ti-rich particles, in all the 800H/800H-TMP samples. Electron backscatter diffraction characterization of GB12 indicated the recovery of the lath structure, which was generally replaced by an equiaxed grain structure. Transmission electron microscopy (TEM) characterization showed the presence of frequent M 23 C 6 (M = primarily Cr), MX (M = primarily V), spherical Nb(C,N) precipitates, and occasional Laves phase precipitates in the G92-2b samples. MX precipitates with sizes of 20-30 nm were observed at boundaries of smaller grains, indicating the pinning effect of the V-rich precipitates. The lath structure recovery was more evident at the higher irradiation temperatures (683.3-~720°C), with decreased densities of line dislocations and M23C6 precipitates. The irradiated T91 (TA04) showed the growth of M23C6 precipitates to 101 ± 40 nm from the initial 68 ± 22 nm in the unirradiated condition. Dislocation loops of both {100} and {111} types were present in TA04. TEM characterization was also performed on the irradiated 800H (N4, N5, N6, and AR2) and 800H-TMP (P4, P5, P6, and HG1). Accumulation of M 23 C 6 precipitates at grain boundaries was observed in all the xii 800H/800H-TMP samples, and the presence of Ti(C,N) precipitates at grain boundaries and in the matrix was observed in the irradiated 800H-TMP. Some Ti(C,N) precipitates are embedded in the M 23 C 6 precipitates, maintaining specific orientation relationships between the precipitates and between the precipitate and matrix. In addition, nanoscale Si-rich clusters were observed in the matrix of all the 800H/800H-TMP samples, with EDS Si maps tending to have a lower contrast in 800H-TMP samples. Atom probe tomography was conducted on the same samples, supported by a Rapid Turnaround Examination project under Nuclear Science User Facilities. The results are being analyzed to be integrated with the TEM results for a confident description of the γ’ precipitates. Dislocation loops also formed in all the 800H/800H-TMP samples. The density and the average size of dislocation loops were quantified to be in the order of 10 22 – 10 23 m -3 and 11.7 – 15.9 nm, respectively, in the ATR-irradiated 800H/800H-TMP samples. The loop densities in irradiated 800H were higher than that in irradiated 800H-TMP under the same irradiation conditions. Further systematic data analyses, together with some complementary experiments, will be pursued for these samples to foster peer-reviewed journal article publications.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Effects of Wind Shear and Aerosol Conditions on the Organization of Precipitating Marine Stratocumulus Clouds

Here this study examines how wind shear affects precipitating marine stratocumulus clouds under different cloud droplet number concentrations (N d ). We performed a series of large eddy simulations (LES) of nocturnal marine stratocumulus clouds using Cloud Model 1 (CM1). The simulations show that N d is the dominant factor for cloud cellular organization in this cloud regime rather than wind shear. Low N d characterizes the open cellular structure with a high in-cloud liquid water path (LWP). When wind shear is increased, the cloud fraction tends to decrease along with LWP, suggesting the cloud top region is significantly influenced by the entrainment and mixing of dry air from the free troposphere. We also examine cold pools in open and closed cellular clouds. Open-cell clouds produce larger and deeper cold pools compared to closed-cell clouds. Interestingly, cold pools can exist without surface precipitation and are produced by evaporation of light precipitation (drizzle) below the cloud base with weak downdrafts. The evaporation of raindrops and drizzle play an important role in initiating new convection, particularly where colliding outflows occur downstream of the cloud. This secondary convection contributes to the development and maintenance of the cloud cellular organization and formation.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Hydroxyapatite/TiO 2 Nanomaterial with Defined Microstructural and Good Antimicrobial Properties

Due to the growing number of people infected with the new coronavirus globally, which weakens immunity, there has been an increase in bacterial infections. Hence, knowledge about simple and low-cost synthesis methods of materials with good structural and antimicrobial properties is of great importance. A material obtained through the combination of a nanoscale hydroxyapatite material (with good biocompatibility) and titanium dioxide (with good degradation properties of organic molecules) can absorb and decompose bacteria. In this investigation, three different synthesis routes used to prepare hydroxyapatite/titanium dioxide nanomaterials are examined. The morphology and semiquantitative chemical composition are characterized by scanning electron microscopy with energy dispersive X-ray analysis (SEM-EDX). The obtained materials’ phase and structural characterization are determined using the X-ray powder diffraction method (XRD). The crystallite sizes of the obtained materials are in the range of 8 nm to 15 nm. Based on XRD peak positions, the hexagonal hydroxyapatite phases are formed in all samples along with TiO 2 anatase and rutile phases. According to SEM and TEM analyses, the morphology of the prepared samples differs depending on the synthesis route. The EDX analysis confirmed the presence of Ti, Ca, P, and O in the obtained materials. The IR spectroscopy verified the vibration bands characteristic for HAp and titanium. The investigated materials show excellent antimicrobial and photocatalytic properties.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

Mild Acetylation and Solubilization of Ground Whole Plant Cell Walls in EmimAc: A Method for Solution-State NMR in DMSO-d6

Lignocellulosic biomass is mainly composed of polysaccharides and lignin. The complexity and diversity of the plant cell wall polymers makes it difficult to isolate the components in pure form for characterization. Many current approaches to analyzing lignocellulose structure, which involve sequential extraction and characterization of the resulting fractions, are time-consuming and labor-intensive. The present study describes a new and facile system for rationally derivatizing and dissolving coarsely ground plant cell wall materials. Using ionic liquids (EmimAc) and dichloroacetyl chloride as a solvent/reagent produced mildly acetylated whole cell walls without significant degradation. The acetylated products were soluble in DMSO-d6 from which they can be characterized by solution-state two-dimensional nuclear magnetic resonance (2D NMR) spectrometry. A distinct advantage of the procedure is that it realizes the dissolution of whole lignocellulosic materials without requiring harsh ball-milling, thereby allowing the acquisition of high-resolution 2D NMR spectra to revealing structural details of the main components (lignin and polysaccharides). The method is therefore beneficial to understanding the composition and structure of biomass aimed at its improved utilization.

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

The effects of warming and soil chemistry on bacterial community structure in Arctic tundra soils

Soil microbial communities in the Arctic play a critical role in regulating the global carbon (C) cycle. Vast amounts of C are stored in northern latitude soils, and rising temperatures in the Arctic threaten to thaw permafrost, making relatively inaccessible C sources more available for mineralization by soil microbes. Few studies have characterized how microbial community structure responds to thawing permafrost in the context of varying soil chemistries associated with contrasting tundra landscapes. Here, we subjected active layer and permafrost soils from upland and lowland tundra sites on the North Slope of Alaska to a soil-warming incubation experiment and compared soil bacterial community profiles (obtained by 16S rRNA amplicon sequencing) before and after incubation. The influence of soil composition (characterized by mid-infrared [MIR] spectroscopy) on bacterial community structure and class abundance was analyzed using redundancy and correlation analyses. We found increased abundances of Alphaproteobacteria, Gammaproteobacteria, and Bacteroidetes [Sphingobacteriia] post incubation, particularly in permafrost soils. The categorical descriptors site and soil layer had the most explanatory power in our predictive models of bacterial community structure, highlighting the close relationship between soil bacteria and the soil environment. Specific soil chemical attributes characterizing the soil environments that were found to be the best predictors include MIR spectral bands associated with inorganic C, silicates, amide II (C=N stretch), and carboxylics (C-O stretch), and MIR peak ratios representing C substrate quality. Overall, these results further characterize soil bacterial community shifts that may occur as a frozen environment with limited access to C sources, such as is found in undisturbed permafrost, transitions to warmer and more C-available environments, such as is predicted in thawing permafrost due to climate change.

16S rRNA sequencing↗
DOE OSTI2023

Chemical Signatures of Seasonally Unique Anthropogenic Influences on Organic Aerosol Composition in the Central Amazon

Urbanization and fires perturb the quantities and composition of fine organic aerosol in the central Amazon, with ramifications for radiative forcing and public health. These disturbances include not only direct emissions of particulates and secondary organic aerosol (SOA) precursors, but also changes in the pathways through which biogenic precursors form SOA. The composition of ambient organic aerosol is complex and incompletely characterized, encompassing millions of potential structures relatively few of which have been synthesized and characterized. Through analysis of submicron aerosol samples from the Green Ocean Amazon (GoAmazon2014/5) field campaign by two-dimensional gas chromatography coupled with machine learning, ~1300 unique compounds were traced and characterized over two seasons. Fires and urban emissions produced chemically and interseasonally distinct impacts on product signatures, with only ~50% of compounds observed in both seasons. Seasonally unique populations point to the importance of aqueous processing in Amazonian aerosol ageing, but further mechanistic insights are impeded by limited product identity knowledge. Further, less than 10% of compounds were identifiable at an isomer-specific level. Overall, the findings (i) provide compositional characterization of anthropogenic influence on submicron organic aerosol in the Amazon, (ii) identify key season-to-season differences in chemical signatures, and (iii) highlight high-priority knowledge gaps in current speciated knowledge.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Investigation of Site Amplifications Using Ambient-Noise-Derived Shallow Velocity Structures Under a Dense Array in Oklahoma

The shear-wave velocity (V S ) structure plays an important role in characterizing site amplification. The Large-n Seismic Survey in Oklahoma (LASSO; 1820 stations) revealed large vertical ground-motion variability in a 25 km × 32 km area in northern Oklahoma. The LASSO array has a relatively simple and flat topography, typical in a sedimentary basin environment in the central United States. In this study, we use the dense array to investigate the velocity structure under the LASSO array and how vertical ground motions relate to the shallow-to-deep structures. We extract the fundamental-mode Rayleigh wave by cross-correlating one month of ambient noise (0.7–5 Hz). We use double-beamforming to measure the group and phase velocities and anisotropy. By jointly inverting the group and phase velocities, we obtain the V S structure. Here, we observe correlations between V S at depths of 0.1–1.5 km and vertical ground motions using sites on the stiffer Permian formations. The shallow Quaternary alluvium and terrace deposits can amplify vertical ground motions by a factor of 2–4.5 between 2 and 25 Hz and attenuate signals above 25 Hz. We use 1D V S profiles to simulate the SV-wave transfer functions. An average V S of 250 m/s in the upper 20–40 m may cause the observed amplification between 2 and 40 Hz. V S estimated by topographic slopes cannot predict the relative amplification. Our results highlight the large variability of site-dependent ground motion in a small local region and the importance of characterizing shallow structures to estimate seismic hazards. Small thickness variations of the shallow formation can significantly change the resonance amplitude and frequency, which likely reduces the coherency of the Rayleigh waves extracted from ambient noise.

Chang, Hilary [Massachusetts Inst. of Technology (↗
DOE OSTI2021

Experimental demonstration of novel beam characterization using a polarizable X-band transverse deflection structure

The PolariX TDS (Polarizable X-Band Transverse Deflection Structure) is an innovative TDS-design operating in the X-band frequency-range. The design gives full control of the streaking plane, which can be tuned in order to characterize the projections of the beam distribution onto arbitrary transverse axes. This novel feature opens up new opportunities for detailed characterization of the electron beam. In this paper we present first measurements of the Polarix TDS at the FLASHForward beamline at DESY, including three-dimensional reconstruction of the charge-density distribution of the bunch and slice emittance measurements in both transverse directions. The experimental results open the path toward novel and more extensive beam characterization in the direction of multi-dimensional-beam-phase-space reconstruction.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2022

X-ray nanodiffraction imaging reveals distinct nanoscopic dynamics of an ultrafast phase transition

Significance Phase transitions, the changes between states of matter with distinct electronic, magnetic, or structural properties, are at the center of condensed matter physics and underlie valuable technologies. First-order phase transitions are intrinsically heterogeneous. When driven by ultrashort excitation, nanoscale phase regions evolve rapidly, which has posed a significant experimental challenge to characterize. The newly developed laser-pumped X-ray nanodiffraction imaging technique reported here has simultaneous 100-ps temporal and 25-nm spatial resolutions. This approach reveals pathways of the nanoscale structural rearrangement upon ultrafast optical excitation, different from those transitions under slowly varying parameters. The spatiotemporally resolved structural characterization provides crucial nanoscopic insights into ultrafast phase transitions and opens opportunities for controlling nanoscale phases on ultrafast time scales.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Influence of Steric and Electronic Properties of P2 Groups on Covalent Inhibitor Binding to SARS-CoV-2 Main Protease

The main protease (MPro) of SARS-CoV-2 is a critical enzyme required for viral replication, making it a prime target for antiviral drug development. Covalent inhibitors, which form a stable interaction with the catalytic C145, have demonstrated strong inhibition of MPro, but the influence of steric and electronic properties of P2 substituents, designed to engage the S2 substrate-binding subsite within the MPro active site, on inhibitor binding affinity remains underexplored. Here, in this study, we design and characterize two hybrid covalent inhibitors, BBH-3 and BBH-4, and present their X-ray crystallographic structures in complex with MPro, providing molecular insights into how their distinct P2 groups, a dichlorobenzyl moiety in BBH-3 and an adamantyl substituent in BBH-4, affect binding conformation and active site adaptability. Comparative structural analyses with previously characterized inhibitors, including BBH-2 and Mcule-5948770040, reveal how the P2 bulkiness and electronic properties influence active site dynamics, particularly through interactions with the S2 and S5 subsites. The P2 group of BBH-3 induces conformational shifts in the S2 helix and the S5 loop, while BBH-4 displaces M49, stabilizing its binding through hydrophobic interactions. Isothermal titration calorimetry further elucidates the impact of P2 modifications on inhibitor affinity, revealing a delicate balance between enthalpic and entropic contributions. The data demonstrate that BBH-3 exhibits less favorable binding, affirming that dichlorobenzyl substitution at the P2 position has a more negative impact on the affinity for MPro than bulky saturated cyclic groups. This underscores the feature that MPro active site malleability may be accompanied by a conformational strain.

SARS-CoV-2↗
DOE OSTI2025

Programmable exploration of magnetic states in Lieb-kagome interpolated lattices

We investigate a hybrid modeling framework in which a quantum annealer is used to simulate magnetic interactions in molecular qubit lattices inspired by experimentally realizable systems. Using phthalocyanine assemblies as a structurally constrained prototype, we model a continuous deformation from a Lieb to a kagome lattice, revealing frustration-driven disorder and magnetic field-induced reordering in the spin structure. Here, the goal is to show how a quantum annealer can operate as a physically instantiated, programmable platform to emulate experimentally relevant lattice deformations and produce observables in a manner analogous to an experimental measurement, enabling the characterization of magnetic arrangements beyond the reach of current molecular architectures. This surrogate modeling approach offers a pathway to explore and iteratively design tunable magnetic states in synthetic materials. The synthetic design, structural characterization, and quantum simulation framework established here defines a modular and scalable paradigm for probing the limits of engineered matter across chemistry, condensed matter, and quantum information science.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2024

Structure and identification of the native PLP synthase complex from Methanosarcina acetivorans lysate

Many protein-protein interactions behave differently in biochemically purified forms as compared to their in vivo states. As such, determining native protein structures may elucidate structural states previously unknown for even well-characterized proteins. Here, we apply the bottom-up structural proteomics method, cryoID , toward a model methanogenic archaeon. While they are keystone organisms in the global carbon cycle and active members of the human microbiome, there is a general lack of characterization of methanogen enzyme structure and function. Through the cryoID approach, we successfully reconstructed and identified the native Methanosarcina acetivorans pyridoxal 5′-phosphate (PLP) synthase (PdxS) complex directly from cryogenic electron microscopy (cryo-EM) images of fractionated cellular lysate. We found that the native PdxS complex exists as a homo-dodecamer of PdxS subunits, and the previously proposed supracomplex containing both the synthase (PdxS) and glutaminase (PdxT) was not observed in cellular lysate. Our structure shows that the native PdxS monomer fashions a single 8α/8β TIM-barrel domain, surrounded by seven additional helices to mediate solvent and interface contacts. A density is present at the active site in the cryo-EM map and is interpreted as ribose 5-phosphate. In addition to being the first reconstruction of the PdxS enzyme from a heterogeneous cellular sample, our results reveal a departure from previously published archaeal PdxS crystal structures, lacking the 37-amino-acid insertion present in these prior cases. This study demonstrates the potential of applying the cryoID workflow to capture native structural states at atomic resolution for archaeal systems, for which traditional biochemical sample preparation is nontrivial.

Methanosarcina acetivorans↗