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At least 199 records · Page 11
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Probing Multiconfigurational States by Spectroscopy: The Cerium XAS L 3 ‐edge Puzzle

Abstract The Ce L 3 edge XAS spectra of CeO 2 and cerocene [Ce(C 8 H 8 ) 2 ] were calculated with relativistic ab‐initio multireference wavefunction approaches capable of reproducing the observed spectra accurately. The study aims to resolve the decades‐long puzzle regarding the relationship between the number and relative intensities of the XAS peaks and the 4f electron occupation in the ground state (GS) versus the core‐excited states (ESs). CeO 2 and cerocene exemplify the different roles of covalent bonding and wavefunction configurational composition in the observed intensity patterns. Good agreement is found between the calculated GS 4f‐shell occupations and the value derived from XAS measurements using peak areas ( n f ). The identity of the two‐peaked Ce L 3 edge is fully rationalized from the perspective of the relaxed wavefunctions for the GS and core ESs. The states underlying the different peaks differ from each other in a surprisingly simple way that can be associated with 4f 1 vs. 4f 0 sub‐configurations. Furthermore, part of one of the cerocene spectral peaks is associated with 4f 2 sub‐configurations. The pattern therefore reveals excited states that can be interpreted in terms of Ce IV and III oxidation numbers, as long assumed, with Ce II states additionally appearing in the cerocene spectrum. While this work demonstrates the rough accuracy of the conventional approach to determining n f from Ce L 3 ‐edge XAS, limitations are highlighted in terms of the ultimate accuracy of this approach and the potential of observing new types of excited states. The need to determine the sources of n f by calculations, is stressed.

Sergentu, Dumitru‐Claudiu↗
DOE OSTI2022

Efficient Electrochemical Reduction of CO 2 to Formate in Methanol Solutions by Mn‐Functionalized Electrodes in the Presence of Amines**

Carbon cloth electrode modified by covalently attaching a manganese organometallic catalyst is used as cathode for the electrochemical reduction of CO 2 in methanol solutions. Six different industrial amines are employed as co-catalyst in millimolar concentrations to deliver a series of new reactive system. While such absorbents were so far believed to provide a CO 2 reservoir and act as sacrificial proton source, we herein demonstrate that this role can be played by methanol, and that the adduct formed between CO 2 and the amine can act as an effector or inhibitor toward the catalyst, thereby enhancing or reducing the production of formate. Pentamethyldiethylentriamine (PMDETA), identified as the best effector in our series, converts CO 2 in wet methanolic solution into bisammonium bicarbonate. Computational studies revealed that this adduct is responsible for a barrierless transformation of CO 2 to formate by the reduced form of the Mn catalyst covalently bonded to the electrode surface. As a consequence, selectivity can be switched on demand from CO to formate anion, and in the case of (PMDETA) an impressive TON HCOO- of 2.8×10 4 can be reached. This new valuable knowledge on an integrated capture and utilization system paves the way toward more efficient transformation of CO 2 into liquid fuel.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Development of the Safe and Broad‐Spectrum Aldehyde and Ketoamide Mpro inhibitors Derived from the Constrained α, γ‐AA Peptide Scaffold

Abstract SARS‐CoV‐2 is still wreaking havoc all over the world with surging morbidity and high mortality. The main protease (M pro ) is essential in the replication of SARS‐CoV‐2, enabling itself an active target for antiviral development. Herein, we reported the design and synthesis of a new class of peptidomimetics‐constrained α, γ‐AA peptides, based on which a series of aldehyde and ketoamide inhibitors of the M pro of SARS‐CoV‐2 were prepared. The lead compounds showed excellent inhibitory activity in the FRET‐based M pro enzymatic assay not only for the M pro of SARS‐CoV‐2 but also for SARS‐CoV and MERS‐CoV, along with HCoVs like HCoV‐OC43, HCoV‐229E, HCoV‐NL63 and HKU1. The X‐ray crystallographic results demonstrated that our compounds form a covalent bond with the catalytic Cys145. They also demonstrated effective antiviral activity against live SARS‐CoV‐2. Overall, the results suggest that α, γ‐AA peptide could be a promising molecular scaffold in designing novel M pro inhibitors of SARS‐CoV‐2 and other coronaviruses.

Chemistry↗
DOE OSTI2023

Endowing Polythioester Vitrimer with Intrinsic Crystallinity and Chemical Recyclability

Abstract Technologically important thermosets face a long‐standing end‐of‐life (EoL) problem of non‐reprocessability, a more sustainable solution of which has resolved to nascent vitrimers that can merge the robust material properties of thermosets and the reprocessability of thermoplastics. However, the lifecycle of vitrimers is still finite, as they often suffer from significant deterioration of mechanical performance following multiple reprocessing cycles, analogous to mechanical recycling, and they often show undesired creep under working conditions. To address these two key limitations, we have developed a cross‐linked semi‐crystalline polythioester with both dynamic covalent bonds and intrinsic crystallinity and chemical recyclability, affording a vitrimeric system that exhibits not only reprocessability and crystallinity‐restricted creep but also complete chemical recyclability to initial monomer by catalyzed depolymerization in solution or bulk. Therefore, reported herein is an “infinite” vitrimer system that is empowered with a facile closed‐loop EoL option once serial reprocessing deteriorates performance and the material can no longer meet the application requirements. Specifically, the polythioester vitrimer was constructed by copolymerization of a bicyclic thioester with a bis‐dithiolane, producing dynamically cross‐linked polythioesters with excellent property tunability, from amorphous to semi‐crystalline states and melting transition temperatures from 91 to 178 °C.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Uncovering Sequence and Structural Characteristics of Fungal Expansin‐Related Proteins With Potential to Drive Substrate Targeting

Expansins loosen plant cell wall networks through disrupting non-covalent bonds between cellulose microfibrils and matrix polysaccharides. Whereas expansins were first discovered in plants, expansin-related proteins have since been identified in bacteria and fungi. The biological function of microbial expansins remains unclear; however, several studies have shown distinct binding preferences toward different structural polysaccharides. Earlier studies of bacterial expansin-related proteins uncovered sequence and structural features that correlate to substrate binding. Herein, 20 fungal expansin-related sequences were recombinantly produced in Komagataella phaffii, and the purified proteins were compared in terms of substrate binding to cellulosic and chitinous substrates. The impact of pH on the zeta potential of prioritized substrates was also measured, and Principal Component Analysis was performed to uncover correlations between protein characteristics (e.g., pI, hydrophobicity, surface charge distribution) and measured substrate binding preferences. Whereas acidic proteins with a predicted pI less than 5.0 preferentially bound to chitin, basic proteins with pI greater than 8.0 preferentially bound to xylan and xylan-containing fiber. Similar to many cellulases, binding to cellulose was correlated to relatively high aromatic amino acid content in the protein sequence and presence of a carbohydrate binding module (CBM), which in the case of expansins is a C-terminal CBM63. Whereas overall sequence characteristics could be correlated to substrate binding preference, the identity of amino acids occupying conserved positions that impact protein activity was better correlated with loosenin versus expansin classifications.

chitin↗
DOE OSTI2023

Effect of Methyl Groups on Formation of Ordered or Layered Graphitic Materials from Aromatic Molecules

Abstract Developing functionally complex carbon materials from small aromatic molecules requires an understanding of how the chemistry and structure of its constituent molecules evolve and crosslink, to achieve a tailorable set of functional properties. Here, molecular dynamics (MD) simulations are used to isolate the effect of methyl groups on condensation reactions during the oxidative process and evaluate the impact on elastic modulus by considering three monodisperse pyrene‐based systems with increasing methyl group fraction. A parameter to quantify the reaction progression is designed by computing the number of new covalent bonds formed. Utilizing the previously developed MD framework, it is found that increasing methylation leads to an almost doubling of bond formation, a larger fraction of the new bonds oriented in the direction of tensile stress, and a higher basal plane alignment of the precursor molecules along the direction of tensile stress, resulting in enhanced tensile modulus. Additionally, via experiments, it is demonstrated that precursors with a higher fraction of methyl groups result in a higher alignment of molecules. Moreover, increased methylation results in the lower spread of single molecule alignment which may lead to smaller variations in tensile modulus and more consistent properties in carbon materials derived from methyl‐rich precursors.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Hierarchically Structured Vitrimer Biocomposites for Sustainable Manufacturing

Polymers containing dynamic covalent bonds (DCBs) exhibit thermoplastic-like flow above their topology freezing temperature (T v ) while maintaining thermoset-like properties below it, making them promising for sustainable manufacturing. However, their large-scale adoption remains limited due to challenges in accurately determining T v and achieving efficient fiber-matrix bonding in composite applications. Here, hierarchically structured epoxy-anhydride-based polyester vitrimer composites reinforced with cellulosic filaments is demonstrated, where hydroxyl groups on fiber surfaces participate directly in transesterification with the matrix. Further, this dynamic interfacial bonding delivers exceptional mechanical properties, including ≈70 MPa shear strength and >10% strain-to-failure, while enabling thermal malleability. Using a combination of nuclear magnetic resonance and nano-infrared spectroscopies, direct evidence is provided that chemical bond exchange begins well below the conventionally measured T v , supporting the hypothesis that rheologically determined T v reflects a combination of chemical exchange and frictional dynamics rather than a discrete transition. The composites demonstrate excellent processability through vacuum-assisted resin transfer molding and maintain >90% of their mechanical properties after multiple thermal reforming cycles. These findings advance both the fundamental understanding of vitrimeric transitions and the practical development of sustainable, high-performance composite materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

A New Platform for Twistronics: Perovskite Moiré Superlattices Beyond van der Waals

Moiré superlattices have reshaped condensed‐matter physics by enabling twist‐angle engineering of electronic and excitonic states, traditionally in van der Waals (vdW) systems. This Perspective focuses on perovskites as a transformative non‐van der Waals (non‐vdW) platform for twistronics. These materials are distinguished by ionic‐covalent bonding and soft octahedral lattices that support deep moiré potentials (≈100–200 meV), which in turn yield bright, room‐temperature excitons and tunable quantum phenomena. We organize recent advances into two core classes: (i) moiré superlattices constructed from 2D Ruddlesden‐Popper (RP) perovskites via spontaneous or guided twisted stacking; and (ii) moiré architectures in 3D perovskite lamellae, achieved through topotactic 2D RP‐to‐3D conversion and ligand‐induced self‐assembly. Key experimental observations in these systems include twist‐tunable moiré periods, suppressed exciton–exciton annihilation, flat band‐like transport, and ferroelectric vortex lattices in their oxide perovskite counterparts. Here, we outline key bottlenecks, including defects arising during phase conversion, stringent lattice‐matching requirements, and the absence of in situ twist metrology, and highlight opportunities in lattice‐mismatched heterostructures and multifunctional quantum‐optoelectronic devices. Collectively, these advances establish perovskite moiré systems as a critical bridge between fundamental moiré physics and room‐temperature technological applications.

2D Ruddlesden–Popper perovskites↗
DOE OSTI2024

Camelina circRNA landscape: Implications for gene regulation and fatty acid metabolism

Abstract Circular RNAs (circRNAs) are closed‐loop RNAs forming a covalent bond between their 3′ and 5′ ends, the back splice junction (BSJ), rendering them resistant to exonucleases and thus more stable compared to linear RNAs. Identification of circRNAs and distinction from their cognate linear RNA is only possible by sequencing the BSJ that is unique to the circRNA. CircRNAs are involved in the regulation of their cognate RNAs by increasing transcription rates, RNA stability, and alternative splicing. We have identified circRNAs from C. sativa that are associated with the regulation of germination, light response, and lipid metabolism. We sequenced light‐grown and etiolated seedlings after 5 or 7 days post‐germination and identified a total of 3447 circRNAs from 2763 genes. Most circRNAs originate from a single homeolog of the three subgenomes from allohexaploid camelina and correlate with higher ratios of alternative splicing of their cognate genes. A network analysis shows the interactions of select miRNA:circRNA:mRNAs for regulation of transcript stabilities where circRNA can act as a competing endogenous RNA. Several key lipid metabolism genes can generate circRNA, and we confirmed the presence of KASII circRNA as a true circRNA. CircRNA in camelina can be a novel target for breeding and engineering efforts.

Utley, Delecia [Department of Plant and Microbial ↗
DOE OSTI2024

Ion Implantation-Induced Plastic Phenomena in Metallic Alloys

Ion implantation is widely used for doping semiconductors or electroceramic materials and probing material behaviors in extreme radiation environments. However, implanted ions can induce compressive stresses into the host material, which can induce plasticity and mesoscopic deformation. However, these phenomena have almost exclusively been observed in brittle ionic and/or covalently bonded materials. Here, in this study, we present transmission electron microscopy observations of unusual implantation-induced plasticity in two metallic alloys. First, Fe 2+ ions induce dislocation plasticity below the implanted layer in a model Fe-P alloy. Next, He+ ions form pressurized cavities which activate the fcc-to-hcp strain-induced martensitic transformation in Alloy 625. In both cases, the plasticity can be explained by a combination of implanted ions being incorporated into the lattice and the creation of irradiation defects. These findings have significant implications for mechanical testing of ion-implanted layers, while also opening pathways for using ion implantation to tune stress distributions in metallic alloys.

36 MATERIALS SCIENCE↗
DOE OSTI2022

From classical to quantum dynamics of atomic and ionic species interacting with graphene and its analogue

Graphene and its analogues offer a broad range of application opportunities for (opto)-electronics, sensing, catalysis, phase separation, energy conversion and storage, etc. Engineering graphene properties often relies on its controllable functionalization, defect formation and patterning, and reactive gas etching. In this chapter, we survey the dynamics of graphene using classical and quantum-classical dynamics methods. We discuss the reactivity, scattering, and transmission of atomic and ionic species including Ar cluster ion, H/D, and H+/D+ on graphene flakes of various sizes, focusing on the atomic-scale motion and energy dissipation pathways involved in forming and breaking covalent bonding. Discussions on the nuclear quantum effects of light species, the effects of isotopic substitution, and the methodologies for such modeling are also included.

Garashchuk, Sofiya V.↗
DOE OSTI2022

An approach to nearest neighbor analysis of pigment-protein complexes using chemical cross-linking in combination with mass spectrometry

Herein, protein cross-linking is the process of chemically joining two amino acids in a protein or protein complex by a covalent bond. When combined with mass spectrometry, it becomes one of the structural mass spectrometry techniques gaining in importance for deriving valuable three-dimensional structural information on proteins and protein complexes. This platform complements existing structural methods, such as NMR spectroscopy, X-ray crystallography, and cryo-EM. Photosynthetic pigment protein complexes serve as light-energy harvesting systems and perform photochemical conversion as part of the “early events” of photosynthesis. This chapter outlines how to prepare cross-linking pigment protein complex samples for LC-MS/MS analysis, including identification of the cross-linked species, network analysis in a protein complex, and structural modeling and justification.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Distinctive features of structural evolution and thermodynamic response in wide-bandgap semiconductors driven by intense electronic excitation

Radiation-tolerant material selection requires balancing lattice rigidity, defect dynamics, and electronic stability, as shown by covalent SiC outperforming ionic Ga 2 O 3 and GaN under extreme environments. Responding to intense electronic excitation, irradiation-driven phase segregation (β → δ/κ in Ga 2 O 3 ) and core–shell track (disordered structure in GaN), accompanied by elemental redistribution, contrastingly, exceptional radiation tolerance manifested by comparatively minimal lattice distortion (0.17 % strain variation) was demonstrated in SiC. These differential responses are primarily attributed to two fundamental mechanisms: (i) thermodynamic driving forces governing defect migration and phase separation, and (ii) the synergistic effects of robust covalent bonding composition coupled with efficient defect recombination processes. Here, the stronger electron–phonon (e-ph) coupling in Ga 2 O 3 (4.34 × 1018 W m −3 K −1 ) and GaN (3.55 × 10 18 W m −3 K −1 ) enhances lattice energy deposition, triggering thermal spikes (ΔT ≫ T m ) and structural transition behaviors, whereas weaker e-ph coupling in SiC (3.69 × 10 18 W m −3 K −1 ), relatively high thermodynamic parameters and efficient energy dissipation suppress thermal spikes to maintaining lattice integrity. The photoresponse degradation driven by enhanced radiative recombination is dominant in N-doped SiC, while V-doped systems achieve defect-mediated photoconduction optimization characterized by abrupt current transitions, matching fluorescence yield evolutions, and directly connecting defect engineering to optoelectronic performance.

Intense electronic excitation↗
DOE OSTI2023

Promoting reversibility of layered potassium cathode through interstitial doping

With the increasing needs for large-scale and low-cost energy storage devices, Mn-based layered oxide cathodes have achieved considerable researching interests for potassium-ion batteries owing to their high energy density, abundant resource and low toxicity. However, their developments are challenged by the absence of suitable cathode materials to tolerate large-sized K-ion insertion/extraction and the presence of Jahn-Teller distortion of Mn 3+ . To address this issue, here we present a strategy of embedding boron into interstitial tetrahedral sites to obtain a P3-K 0.5 Mn 0.8 Co 0.2 B 0.1 O 2 cathode. Strong B-O covalent bonds facilitate the construction of robust orthorhombic framework and alleviate the undesired elongation of Mn-O bonds, contributing to excellent electrochemical performance. In addition, boron ions are verified to promote the formation of a homogeneous cathode electrolyte interphase layer, improving interfacial stability and realizing highly reversible cycling in a wide voltage range (1.4-4.3 V). This strategy provides a new pathway towards the development of high-performance cathode materials for potassium-ion batteries.

25 ENERGY STORAGE↗
DOE OSTI2023

QMMM 2023: A program for combined quantum mechanical and molecular mechanical modeling and simulations

Combined quantum mechanical and molecular mechanical (QM/MM) methods play an important role in multiscale modeling and simulations. QMMM 2023 is a general-purpose program for single-point calculations, geometry optimizations, transition-state optimizations, and molecular dynamics (MD) at the QM/MM level. It calls a QM package and an MM package to perform the required single-level calculations and combines them into a QM/MM energy by a variety of schemes. QMMM 2023 supports GAMESS-US, Gaussian, and ORCA as QM packages and Tinker as the MM package. Four types of treatments are available for embedding the QM subsystem in the MM environment: mechanical embedding with gas-phase calculations of the QM region, electronic embedding that allows polarization of the QM region by the MM environment, polarizable embedding for mutual polarization of the QM and MM regions, and flexible embedding for both mutual polarization and partial charge transfer between the QM and MM regions. Boundaries between QM and MM regions that pass through covalent bonds can be treated by several methods, including the redistributed charge (RC) scheme, redistributed charge and dipole (RCD) scheme, balanced-RC scheme, balanced-RCD scheme, screened charge scheme that takes account of charge penetration effects, and smeared charge scheme that delocalizes the MM charges near the QM–MM boundary. Geometry optimization can be done using the optimizer implemented in QMMM 2023 or the Berny optimizer in Gaussian through external calls to Gaussian. Molecular dynamics simulations can be performed at the pure-MM level, pure-QM level, fixed-partitioning QM/MM level, and adaptive-partitioning QM/MM level. As a result, the adaptive-partitioning treatments permit on-the-fly relocation of the QM–MM boundary by dynamically reclassifying atoms or groups into the QM or MM subsystems.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

The role of nonmetallic ion substitution in perovskite LaCoO 3 for improved oxygen evolution reaction activity

Transition metal perovskite (ABO 3 ) is an emerging type of oxygen evolution reaction (OER) electrocatalyst that shows reasonably good activity and moderate stability. Although efforts have been made to improve perovskite’ OER performance by various element substitution at A/B-site, the influence of ion, particularly non-metallic ion, substitutions on the OER mechanism are rarely studied. More and more evidence has shown that the metal-center theory has failed to explain lots of OER-related phenomena. Therefore, it is urgent to understand how the cation and anion sites in perovskite determine OER performance. In this work, we used a Fe and P co-doped LaCoO 3 as a model system to explore the influence of substitution in perovskite by combining operando/ex-situ X-ray characterization and density functional theory (DFT). We observed enhanced OER catalytic activities in co-doped materials, which are attributed to the stronger transition-metal-oxygen-bonding-covalency (TMOBC). The detailed analyses by O K-edge XAS, electrochemical performance, and DFT suggest that the hybridization between O 2p and transition metal 3d e g orbitals could be a more credible descriptor of perovskite for OER, which is the combination of e g orbital theory and TMOBC theory. The finding in our work provides insights into the OER catalysis mechanism on metal oxides, which could guide new design of cost-effective oxide electrocatalysts.

25 ENERGY STORAGE↗
DOE OSTI2022

Atomic-scale mechanism of carbon nucleation from a deep crustal fluid by replica exchange reactive molecular dynamics simulation

Here we present a mechanistic model of carbon nucleation and growth from a fluid at elevated temperature (T) and pressure conditions, typical of those found in the shallow Earth’s lithosphere. Our model uses a replica exchange reactive molecular dynamics framework in which molecular configurations are swapped between adjacent T replica at regular intervals according to underlying statistical mechanics. This framework allows predicting complex molecular structures and thermodynamics while remaining computationally efficient. Here we simulate the reactivity of an unstable mixture of CO 2 and CH 4 at 1000 K and 1 GPa. We find that the path to thermodynamic equilibrium is initially entropy-driven, producing a diversity of short-lived species, including various alcohols with intermediate carbon oxidation states. Cyclic and polycyclic radicals that are sometimes resonance-stabilized form next and set the stage for carbon nucleation. The carbon exsolution process releases abundant water, is exothermic and starts with the nucleation of a large aggregate of hydrogenated graphene flakes from covalently bonded polycyclic units. The carbon backbone of this nucleus subsequently grows into a hydrogen-depleted fullerene-like structure, before evolving toward a partially bilayered graphene layer. Overall, our results show that the mechanism of graphitic C formation is certainly not bimolecular, and that it may involve a combination of key condensation and radical chain reactions. This will help understand the isotopic, and reactive characteristics of carbon-bearing fluids during their upward transit through the Earth’s mantle and crust. Moreover, the mechanistic insights outlined here present intriguing similarities with the process of soot and interstellar dust formation, which suggests that the widespread distribution of abiotic polyaromatic and graphitic material on Earth and beyond may reflect the prevalence of a fundamental chemical pathway.

58 GEOSCIENCES↗
DOE OSTI2021

Elucidating the structural properties and reversible regional texture effect of GdB 6 under high pressure

As hard and refractory materials with high chemical resistance and mechanical strength, lanthanide hexaborides (LnB 6 ) have attracted much attention. Among the family of LnB 6 , gadolinium hexaboride (GdB 6 ) occupies a special position due to the half-filled 4f shell of Gd. Here, using in situ synchrotron radiation angle-dispersive X-ray diffraction in a diamond anvil cell at room temperature, the structural stability and compression behavior of GdB 6 are investigated extensively, GdB 6 is observed to be structurally stable up to 73 GPa, and the bulk modulus of 177 GPa is obtained under hydrostatic compression. In this paper, an interesting observation of pressure-induced spotty diffraction rings of GdB6 is reported, its formation mechanism can be well described by the reversible regional texture effect, which highlights the rearrangement of crystal grains under high pressure. The rearrangement mechanism has been well explained by investigating the pressure dependence of full width at half maximum, macro-differential stress and grain size. Collective grain rotation behavior motivated by stress difference is critical for the rearrangement process, the strong isotropy and strong stability of GdB 6 structure also provide necessary conditions for high-pressure grain rotation behavior. These results will help to promote the understanding of high-pressure structural properties of GdB 6 , and provide novel insights on the high-pressure grain behavior in hard materials with strong isotropy and three-dimensional skeleton constituted of strong covalent bonds.

36 MATERIALS SCIENCE↗