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DOE OSTI2025

Structure-performance relationships in lignin-based transesterification vitrimers: The role of lignin structural features

Lignin has been hailed as an ideal renewable alternative for petrochemical-based prepolymers in material synthesis for a sustainable and circular economy, due to its abundant aromatic network and high carbon content. However, the properties and performance of lignin-derived macromolecules are strongly influenced by the lignin itself. While numerous studies have explored the impact of lignin content on the thermomechanical performance of lignin-based vitrimers, literature on how the inherent structural features of lignin affect these properties is scanty. In this study, hardwood organosolv lignin was fractionated in ethyl acetate, ethanol, and acetone to obtain lignin fractions with varying structural characteristics. These fractions were then modified through carboxylation and crosslinked with epoxidized soybean oil (ESO) at a hydroxyl to epoxy group ratio of 1:1 to produce lignin-based transesterification vitrimers (LVs). The thermal properties (i.e. glass transition temperature and thermal stability), tensile strength, storage modulus, and stress relaxation behavior of the LVs were studied and carefully related to the structural features of lignin. The results revealed a positive relationship between strong hydroxyl content in modified lignin and the tensile strength (5.10–9.71 MPa), storage modulus (1099.4 – 1372.8 MPa), crosslinking density, and stress relaxation of the LVs. Additionally, both the storage modulus and tensile strength exhibited a positive relationship with the ratio of rigid linkages in modified lignin, while lignin molecular weight was found to significantly impact the thermal properties of LVs (i.e Tg and thermal stability). This study not only highlights the valorization of lignin in vitrimer synthesis but also provide insights for designing lignin-based materials with tailored properties for specific applications.

Bio-based polymer↗

DOE OSTI2023

Engineering highly stable variants of Corynactis californica green fluorescent proteins

Fluorescent proteins (FPs) are versatile biomarkers that facilitate effective detection and tracking of macromolecules of interest in real time. Engineered FPs such as superfolder green fluorescent protein (sfGFP) and superfolder Cherry (sfCherry) have exceptional refolding capability capable of delivering fluorescent readout in harsh environments where most proteins lose their native functions. Our recent work on the development of a split FP from a species of strawberry anemone, Corynactis californica, delivered pairs of fragments with up to threefold faster complementation than split GFP. We present the biophysical, biochemical, and structural characteristics of five full-length variants derived from these split C. californica GFP (ccGFP). These ccGFP variants are more tolerant under chemical denaturation with up to 8 kcal/mol lower unfolding free energy than that of the sfGFP. It is likely that some of these ccGFP variants could be suitable as biomarkers under more adverse environments where sfGFP fails to survive. A structural analysis suggests explanations of the variations in stabilities among the ccGFP variants.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

Effects of Composition and Oxidation States on the Structures of Chromium-Containing Sodium Silicate Glasses: Molecular Dynamics Simulations using Machine Learning Interatomic Potentials

Chromium represents a significant challenge for the vitrification of high-level nuclear waste into silicate and borosilicate glasses due to its low solubility and variable oxidation states, which can limit the waste loading due to promotion of crystallization or phase separation during processing. In this study, we modeled chromium containing silicate glasses using molecular dynamics simulations with three machine learning interatomic potentials (MLIPs), MACE, CHGNet, and PFP were employed, to gain insights on glass composition and oxidation states on the structures of these glasses. One of the goals is to evaluate their ability of these MLIPs to accurately represent the general structure of silicate glasses and chromium local environments as a function of chromium oxidation states. Density Functional Theory (DFT) based calculations and experimental data such as neutron structure factors were used to validate the structural models. It was found that the foundation models of all three MLIPs are able to reproduce general structural features of the sodium silicate glass structure consistent with experimental and DFT data, but only CHGNet and PFP can accurately capture the oxidation states and local environment of chromium: tetrahedral for Cr6+ and octahedral for Cr3+. Furthermore, we studied the effect of varying Cr3+/ Cr6+ (Cr3+/Crtotal) ratio and total chromium content using PFP. Our results show that Cr6+ enhances network polymerization by reducing non-bridging oxygens through Na? charge compensation required due to the formation of chromate (CrO42-) species, while Cr³? acts as a network modifier that disrupts connectivity. System size effects on the structural characteristics and chromium environments were also tested using the PFP potential. This work highlights the importance of careful validation on the precision, transferability, and potential of MLIPs for modeling glasses containing transition metal elements that can exist in multiple oxidation states. It is also encouraging to see the foundational models are all three MLFFs are able to reproduce the basic sodium silicate glass structures, while suggesting additional training or refining is needed to improve the description of more complex systems containing transition metals.

Puga, Christina L.↗

DOE OSTI2023

Study of unripe and inferior banana flours pre-gelatinized by four different physical methods

This study aimed to prepare the pre-gelatinized banana flours and compare the effects of four physical treatment methods (autoclaving, microwave, ultrasound, and heat-moisture) on the digestive and structural characteristics of unripe and inferior banana flours. After the four physical treatments, the resistant starch (RS) content values of unripe and inferior banana flours were decreased from 96.85% (RS2) to 28.99–48.37% (RS2 + RS3), while C∞ and k values were increased from 5.90% and 0.039 min −1 to 56.22–74.58% and 0.040–0.059 min −1 , respectively. The gelatinization enthalpy (ΔHg) and I 1047/1022 ratio (short-range ordered crystalline structures) were decreased from 15.19 J/g and 1.0139 to 12.01–13.72 J/g, 0.9275–0.9811, respectively. The relative crystallinity decreased from 36.25% to 21.69–26.30%, and the XRD patterns of ultrasound (UT) and heat-moisture (HMT) treatment flours maintained the C-type, but those samples pre-gelatinized by autoclave (AT) and microwave (MT) treatment were changed to C + V-type, and heat-moisture (HMT) treatment was changed to A-type. The surface of pre-gelatinized samples was rough, and MT and HMT showed large amorphous holes. The above changes in structure further confirmed the results of digestibility. According to the experimental results, UT was more suitable for processing unripe and inferior banana flours as UT had a higher RS content and thermal gelatinization temperatures, a lower degree and rate of hydrolysis, and a more crystalline structure. The study can provide a theoretical basis for developing and utilizing unripe and inferior banana flours.

Zhang, Siwei↗

DOE OSTI2020

Coexistence of Reflection Asymmetric and Symmetric Shapes in $^{144}\mathrm{Ba}$

Level structures in the neutron-rich $^{144}\mathrm{Ba}$ nucleus have been reinvestigated by measuring prompt gamma rays in the spontaneous fission of $^{252}\mathrm{Cf}$. The previous $s = +1$ octupole band structure with reflection asymmetric shape has been expanded, and a side quadrupole band structure based on a $3^+$ state with reflection symmetric shape is identified. Thus, the results show the coexistence of reflection asymmetric and symmetric shapes in $^{144}\mathrm{Ba}$. This is a first identification of such a shape coexistence structure in a nuclear structure. Finally, the other structural characteristics are discussed.

144Ba↗

DOE OSTI2025

The structural basis for the broad aldehyde specificity of the aminoaldehyde dehydrogenase PauC from the human pathogen Pseudomonas aeruginosa

Abstract Despite significant differences in size and formal charge, the aldehyde dehydrogenasePaPauC (PA5312) fromPseudomonas aeruginosaPAO1 efficiently catalyzes the NAD + ‐dependent oxidation of the aminoaldehydes formed in polyamines degradation. We report here thatPaPauC also oxidizes 4‐guanidinebutyraldehyde, formed in one arginine degradation pathway, trimethylaminobutyraldehyde, of unknown metabolic origin, and indole‐3‐acetaldehyde, a precursor of the plant growth‐promoting hormone indoleacetic acid.PaPauC has been proposed as a potential target for combatingP. aeruginosa. However, understanding its structure–function relationships, crucial for developing specific inhibitors, is lacking. Using X‐ray crystallography, we identified the structural characteristics that determinePaPauC broad aldehyde specificity: a spacious aldehyde‐entrance tunnel and six active‐site residues. Docking simulations, site‐directed mutagenesis, and kinetic analyses support the interactions of Lys479 with glutamylated aminoaldehydes; Phe169, Trp176, and Phe467 with amino and guanidinium groups through cation–π interactions and with the indole group via NH–π and CH–π interactions; Asp459 with amino and indole groups; and Thr303 with amide and guanidinium groups. Exploiting the distinctive structural features of thePaPauC active site could aid in developing specific inhibitors to combatP. aeruginosainfections in humans and animals, as well as in preventing its colonization of plants, which are abundantP. aeruginosareservoirs and, therefore, a significant source of human infections.

Biochemistry & Molecular Biology↗

DOE OSTI2020

A review of the application of 2D isotropic-anisotropic correlation NMR spectroscopy in structural studies of chalcogenide glasses

The application of solid-state high-resolution NMR spectroscopy in the structural investigation of chalcogenide glasses in Ge/As/P/Si-X (X = S, Se,Te) systems has remained challenging even for the spin-1/2 nuclides ( 29 Si, 31 P, 77 Se, 125 Te), owing to their low natural abundance (except for 31 P), slow spin-lattice relaxation rate and large CSA and chemical shift distribution induced line broadening effects. However, most of these deleterious effects can be successfully overcome in two-dimensional (2D) isotropic-anisotropic correlation NMR experiments, especially when performed at high magnetic field and in conjunction with the Car-Purcell-Meiboom-Gill (CPMG) echo train acquisition. Here, we present a short introduction to the basic principles of such experiments and review their applications over the last decade in deciphering various short- and intermediate- range structural characteristics of chalcogenide glasses in S-Se, Se-Te, Ge-Se, As-Se and Si-Se systems as well as in investigating the molecular dynamics in a P-Se supercooled liquid. We anticipate possible future applications of these 2D isotropic-anisotropic correlation NMR experiments, particularly in conjunction with density functional theory-based calculations of NMR chemical shift tensor parameters and additional signal enhancement schemes, in addressing complex structural correlations and distributions in chalcogenide glasses.

2D NMR↗

DOE OSTI2025

Strain release by 3D atomic misfit in fivefold twinned icosahedral nanoparticles with amorphization and dislocations

Multiple twinning to form fivefold twinned nanoparticles in crystal growth is common and has attracted broad attention ranging from crystallography research to physical chemistry and materials science. Lattice-misfit strain and defects in multiple twinned nanoparticles (MTP) are key to understand and tailor their electronic properties. However, the structural defects and related strain distributions in MTPs are poorly understood in three dimensions (3D). Here, we show the 3D atomic misfit and strain relief mechanism in fivefold twinned icosahedral nanoparticles with amorphization and dislocations by using atomic resolution electron tomography. We discover a two-sided heterogeneity in variety of structural characteristics. A nearly ideal crystallographic fivefold face is always found opposite to a less ordered face, forming Janus-like icosahedral nanoparticles with two distinct hemispheres. The disordered amorphous domains release a large amount of strain. Molecular dynamics simulations further reveal the Janus-like icosahedral nanoparticles are prevalent in the MTPs formed in liquid-solid phase transition. This work provides insights on the atomistic models for the modelling of formation mechanisms of fivefold twinned structures and computational simulations of lattice distortions and defects. We anticipate it will inspire future studies on fundamental problems such as twin boundary migration and kinetics of structures in 3D at atomic level.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Structural basis for sensitivity and acquired resistance of fungal cap guanine-N7 methyltransferases to the antifungal antibiotic sinefungin

Abstract The essential enzyme messenger RNA (mRNA) (guanine-N7) methyltransferase catalyzes S-adenosylmethionine (SAM)-dependent conversion of GpppRNA ends to the m7GpppRNA cap structure characteristic of eukaryal mRNAs. The antibiotic sinefungin (SFG) is a SAM analog in which the S-CH3 sulfonium moiety of SAM is replaced by a C-NH2 amine. Available evidence indicates that the antifungal activity of SFG is exerted via inhibition of fungal cap methyltransferase Abd1. Here we report that recombinant Kluyveromyces lactis and Saccharomyces cerevisiae Abd1 are 240-fold and 485-fold more sensitive to inhibition by SFG than by the reaction product S-adenosylhomocysteine (SAH). Crystal structures of K. lactis and S. cerevisiae Abd1 as binary complexes with SAH or SFG and ternary complexes with GTP•SFG highlight how SFG makes two hydrogen bonds from its C-NH2 amine to the guanine-O6 and -N7 atoms of GTP that account for its higher affinity vis-à-vis SAH and SAM. Through a genetic screen to isolate SFG-resistant S. cerevisiae strains, a conserved tyrosine (Tyr416) that interacts with the cap guanine in Abd1 was identified as a key determinant of SFG potency. Tyr416 Abd1 variants confer SFG resistance in vitro by weakening cap-assisted SFG interactions with Abd1. Our study illuminates the basis for the exquisite SFG sensitivity of fungal cap methyltransferases.

Biochemistry & Molecular Biology↗

DOE OSTI2024

Quantification of Native Lignin Structural Features with Gel–Phase 2D–HSQC 0 Reveals Lignin Structural Changes During Extraction

Our ability to study and valorize the lignin fraction of biomass is hampered by the fundamental and still unmet challenge of precisely quantifying native lignin's structural features. Here, we developed a rapid elevated-temperature 1 H– 13 C Heteronuclear Single-Quantum Coherence Zero (HSQC 0 ) NMR method that enables this precise quantification of native lignin structural characteristics even with whole plant cell wall (WPCW) NMR spectroscopy, overcoming fast spin relaxation in the gel phase. We also formulated a Gaussian fitting algorithm to perform automatic and reliable spectral integration. By combining HSQC 0 measurements with yield measurements following depolymerisation, we can confirm the combinatorial nature of radical coupling reactions during biosynthesis leading to a random sequential organization of linkages within a largely linear lignin chain. Such analyses illustrate how this analytical method can greatly facilitate the study of native lignin structure, which can then be used for fundamental studies or to understand lignin depolymerization methods like reductive catalytic fractionation or aldehyde-assisted fractionation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Quantification of Native Lignin Structural Features with Gel–Phase 2D–HSQC 0 Reveals Lignin Structural Changes During Extraction

09 BIOMASS FUELS↗

DOE OSTI2022

Multiple experimental studies of pore structure and mineral grain sizes of the Woodford shale in southern Oklahoma, USA

Pore structure study is an important part of unconventional shale reservoir characterization, since the pore system provides the primary petroleum storage space and fluid flow pathways. Previous studies have suggested that the pore structure is related to the total organic carbon (TOC) content, mineral compositions, and the maturity of the organic matter (OM). However, few studies have focused on the mineral grains, the primary grains being deposited but before cementation, which are the building blocks of shale. Eight Woodford Shale outcrop samples from southern Oklahoma were chosen to study the effects of mineral grain size on the pore structure characterization, using multiple and complementary experimental approaches, including laser diffraction, mineralogy, TOC, pyrolysis, liquid immersion porosimetry, mercury intrusion porosimetry, gas physisorption, (ultra) small angle X-ray scattering, scanning electron microscopy, and spontaneous imbibition. The results from different experiments of eight samples show that the Woodford Shale has the mean mineral grain diameters at 3–6 μm, a wide range of porosity at 3–40% and pore diameters at 50–1,000 nm, and various pore connectivity. Grain size variation was probably caused by the sea-level fluctuation during its deposition, which affect the porosity, pore size distribution, and pore connectivity. With decreasing mineral grain sizes, the porosity tends to increase while the pore connectivity worsens. The results also indicate that OM and carbonates in this low-maturity Woodford Shale could block the pores and decrease the porosity. Coupling with the grain size analyses, the control of depositional environment on grain sizes and subsequent effects on pore structure is identified. The pore structure characteristics over a wide pore-diameter range provided by multiple experiments could improve the understanding of storage space and fluid flow in the Woodford Shale to further increase its petroleum production.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2023

Molecular and Genetic Characterization of Hepatitis B Virus (HBV) among Saudi Chronically HBV-Infected Individuals

The study aimed to characterize the genotype and subgenotypes of HBV circulating in Saudi Arabia, the presence of clinically relevant mutations possibly associated with resistance to antivirals or immune escape phenomena, and the possible impact of mutations in the structural characteristics of HBV polymerase. Plasma samples from 12 Saudi Arabian HBV-infected patients were analyzed using an in-house PCR method and direct sequencing. Saudi patients were infected with mainly subgenotype D1. A number of mutations in the RT gene (correlated to antiviral resistance) and within and outside the major hydrophilic region of the S gene (claimed to influence immunogenicity and be related to immune escape) were observed in almost all patients. Furthermore, the presence of mutations in the S region caused a change in the tertiary structure of the protein compared with the consensus region. Clinical manifestations of HBV infection may change dramatically as a result of viral and host factors: the study of mutations and protein-associated cofactors might define possible aspects relevant for the natural and therapeutic history of HBV infection.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2025

ThO 2 and Th 1– x U x O 2 Nanoscale Materials and Thin Films for Nuclear Science Applications

This study investigates the dynamics and mechanisms of solution combustion synthesis (SCS) for the preparation of nanoscale ThO 2 and Th 1–x U x O 2 materials, utilizing metal nitrates (Th(NO 3 ) 4 and UO 2 (NO 3 ) 2 ) and acetylacetone (C 5 H 8 O 2 ) as reactants dissolved in a 2-methoxyethanol (C 3 H 8 O 2 ) solvent. By combining thermodynamic calculations, dynamic time–temperature profile measurements with differential scanning calorimetry (DSC) and thermogravimetric analysis (TGA), this research reveals how variations in acetylacetone concentration and uranium content influence the structural parameters of the synthesized oxides. The time–temperature measurements show that the heating rate and maximum combustion temperatures are sensitive to acetylacetone concentration. DSC-TGA results indicate shifts in exothermic peak temperatures as the uranium content changes. The complexation between thorium and acetylacetone emerges as a critical factor, impacting combustion parameters and the structural characteristics of the final products. The uniform distribution of Th and U in the Th 1–x U x O 2 solid solution and the formation of nanoscale particles with strained crystallites are considered essential for the low-temperature densification of these materials for nuclear fuel pellet applications. Additionally, high-quality ThO 2 and Th 1–x U x O 2 thin (100–150 nm) films are successfully synthesized via electrospray deposition of combustible solutions followed by a brief period of heat treatment. Furthermore, these films exhibit excellent structural and morphological uniformity, making them ideal candidates for nuclear measurements, irradiation damage studies, and investigations into the physical properties of both pure and mixed oxides.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Selected Negative Linear Compressibilities in the Metal–Organic Framework of [Cu(4,4'-bpy) 2 (H 2 O) 2 ]·SiF 6

Negative linear compressibility (NLC) is a rare high-pressure observation that lattice contraction is accompanied by the structural expansion along a specific direction. Generally, this counterintuitive phenomenon only derives from the intrinsic structural characteristics of materials and cannot be tuned by external perturbations. Searching for an effective method to control NLC effect is still a challenge in both chemical and material science. In this work, we successfully discover and select the NLC behaviors in the metal-organic framework (MOF) of [Cu(4,4'-bpy) 2 (H 2 O) 2 ]·SiF 6 (Cu(bpy)·SiF) through controlling the pressure conditions therein. The NLC effect of Cu(bpy)·SiF originates from the wine-rack mechanism that quasi-square grids transfer to rhombic ones with the structural expansion along the diagonal direction at high pressure. Meanwhile, both of the pressure range and magnitude of the NLC responses are enlarged with optimized pressure conditions. This study not only presents the intriguing selected NLC behaviors of a MOF but also proves the effects of pressure conditions on NLC, which offers promising strategies for further design and applications of NLC materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Subcellular Feature-Based Classification of α and β Cells Using Soft X-ray Tomography

The dysfunction of α and β cells in pancreatic islets can lead to diabetes. Many questions remain on the subcellular organization of islet cells during the progression of disease. Existing three-dimensional cellular mapping approaches face challenges such as time-intensive sample sectioning and subjective cellular identification. To address these challenges, we have developed a subcellular feature-based classification approach, which allows us to identify α and β cells and quantify their subcellular structural characteristics using soft X-ray tomography (SXT). We observed significant differences in whole-cell morphological and organelle statistics between the two cell types. Additionally, we characterize subtle biophysical differences between individual insulin and glucagon vesicles by analyzing vesicle size and molecular density distributions, which were not previously possible using other methods. These sub-vesicular parameters enable us to predict cell types systematically using supervised machine learning. We also visualize distinct vesicle and cell subtypes using Uniform Manifold Approximation and Projection (UMAP) embeddings, which provides us with an innovative approach to explore structural heterogeneity in islet cells. This methodology presents an innovative approach for tracking biologically meaningful heterogeneity in cells that can be applied to any cellular system.

3D cell mapping↗

DOE OSTI2024

Electrochemical control over stoichiometry via cation intercalation into Chevrel-phase sulphides (Cu x Mo 6 S 8 , x = 1-3)

Herein this work presents a systematic investigation of the electrochemical intercalation of aqueous copper cations into the Chevrel phase (CP) Mo 6 S 8 and its effect on the host's electronic and structural characteristics as a function of stoichiometry. The electrochemical potentials at which copper intercalates into the CP Mo 6 S 8 host in 1 M CuSO 4 were identified for Cu x Mo 6 S 8 (x = 1–3) as 0.23 V, 0.11 V, and 0.055 V (vs. Cu/Cu 2+ ) for Cu 1 Mo 6 S 8 , Cu 2 Mo 6 S 8 , and Cu 3 Mo 6 S 8 , respectively, and correlated via ex situ PXRD to stoichiometric content. Potentials were also identified that yield non-stoichiometric phases with traceable Cu content-dependent structural changes. Ab initio DFT calculations were performed to probe thermodynamic stability of Cu x Mo 6 S 8 CP compositions and the metal-to-semiconductor transitions as a function of copper content. Lastly, we demonstrate that the SK-pre-edge intensity is a successful probe for intercalant content: as copper equivalents increase, so does charge transfer to the partially occupied S 3p orbitals, resulting in a decrease in the pre-edge intensity corresponding to the excitation of a S 1s-to-3p/Mo 4d hybridized orbital.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Forest structural complexity and ignition pattern influence simulated prescribed fire effects

Background: Forest structural characteristics, the burning environment, and the choice of ignition pattern each influence prescribed fire behaviors and resulting fire effects; however, few studies examine the influences and interactions of these factors. Understanding how interactions among these drivers can influence prescribed fire behavior and effects is crucial for executing prescribed fires that can safely and effectively meet management objectives. To analyze the interactions between the fuels complex and ignition patterns, we used FIRETEC, a three-dimensional computational fluid dynamics fire behavior model, to simulate fire behavior and effects across a range of horizontal and vertical forest structural complexities. For each forest structure, we then simulated three different prescribed fires each with a unique ignition pattern: strip-head, dot, and alternating dot. Results: Forest structural complexity and ignition pattern affected the proportions of simulated crown scorch, consumption, and damage for prescribed fires in a dry, fire-prone ecosystem. Prescribed fires in forests with complex canopy structures resulted in increased crown consumption, scorch, and damage compared to less spatially complex forests. The choice of using a strip-head ignition pattern over either a dot or alternating-dot pattern increased the degree of crown foliage scorched and damaged, though did not affect the proportion of crown consumed. We found no evidence of an interaction between forest structural complexity and ignition pattern on canopy fuel consumption, scorch, or damage. Conclusions: We found that forest structure and ignition pattern, two powerful drivers of fire behavior that forest managers can readily account for or even manipulate, can be leveraged to influence fire behavior and the resultant fire effects of prescribed fire. These simulation findings have critical implications for how managers can plan and perform forest thinning and prescribed burn treatments to meet risk management or ecological objectives.

54 ENVIRONMENTAL SCIENCES↗