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Results for “Structure elucidation”

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 757 records · Page 42
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Unraveling local structures of Salt-in-Water and Water-in-Salt electrolytes via ab initio molecular dynamics

Water-in-salt electrolytes (WiSE) are attractive for electrochemical energy storage applications owing to their wide electrochemical stability windows and inherent safety. The high concentration of salts is widely known to suppress the decomposition of water, which otherwise limits the stability of conventional aqueous salt-in-water electrolytes (SiWE). Nevertheless, the microstructural features of WiSE that lead to this enhanced stability have not yet been fully elucidated. In this work, ab initio molecular dynamics simulations were performed to study the energetic, structural, and spectroscopic properties of LiTFSI SiWE and WiSE solutions. A detailed mapping of water-water and water-anion hydrogen bonding and cation–anion electrostatic interactions is reported for both electrolytes. Structural features are presented in terms of both radial and spatial distribution functions. Analysis of IR and vibrational power spectra reveal key differences in the intermolecular interactions in SiWE and WiSE that arise from modified solvation shell structures. Finally, the results obtained herein reveal the most important structural and spectroscopic differences between the electrolytes in normal and superconcentrated concentrations.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Metal-Mediated DNA Nanotechnology in 3D: Structural Library by Templated Diffraction

DNA double helices containing metal-mediated DNA (mmDNA) base pairs are constructed from Ag + and Hg 2+ ions between pyrimidine:pyrimidine pairs with the promise of nanoelectronics. Rational design of mmDNA nanomaterials is impractical without a complete lexical and structural description. Here, in this study, the programmability of structural DNA nanotechnology toward its founding mission of self-assembling a diffraction platform for biomolecular structure determination is explored. The tensegrity triangle is employed to build a comprehensive structural library of mmDNA pairs via X-ray diffraction and generalized design rules for mmDNA construction are elucidated. Two binding modes are uncovered: N3-dominant, centrosymmetric pairs and major groove binders driven by 5-position ring modifications. Energy gap calculations show additional levels in the lowest unoccupied molecular orbitals (LUMO) of mmDNA structures, rendering them attractive molecular electronic candidates.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Multiphase, Multiscale Chemomechanics at Extreme Low Temperatures: Battery Electrodes for Operation in a Wide Temperature Range

Understanding the behavior of lithium-ion batteries (LIBs) under extreme conditions, for example, low temperature, is key to broad adoption of LIBs in various application scenarios. LIBs, poor performance at low temperatures is often attributed to the inferior lithium-ion transport in the electrolyte, which has motivated new electrolyte development as well as the battery preheating approach that is popular in electric vehicles. A significant irrevocable capacity loss, however, is not resolved by these measures nor well understood. Herein, multiphase, multiscale chemomechanical behaviors in composite LiNi x Mn y Co z O 2 (NMC, x + y + z = 1) cathodes at extremely low temperatures are systematically elucidated. The low-temperature storage of LIBs can result in irreversible structural damage in active electrodes, which can negatively impact the subsequent battery cycling performance at ambient temperature. Furthermore, beside developing electrolytes that have stable performance, designing batteries for use in a wide temperature range also calls for the development of electrode components that are structurally and morphologically robust when the cell is switched between different temperatures.

25 ENERGY STORAGE↗
DOE OSTI2021

Mass transport in nanoarray monolithic catalysts: An experimental-theory study

Reducing the mass transfer resistance globally of a catalyst is a key to enhancing the catalytic reaction kinetics and fully utilizing the catalyst activity. Despite the success in tailoring the external mass transfer in the widely studied washcoat monoliths, the internal mass transfer resistance is difficult to be reduced due to the requirement of increasing macroporosity while maintaining high specific surface area and mechanical stability. Therefore, nanostructured array-based monolithic catalysts (nanoarray catalysts) have been developed in the past decade as a promising class of structured catalysts that may complement or substitute washcoat catalysts. This work fundamentally elucidates the enhanced mass transport properties of the nanoarray monolithic catalysts by a combination of experimental measurements and theoretical modeling. Using a low-dimensional model, the relative contributions of resistances were quantified in terms of chemical kinetics, internal and external mass transfers based on a probe model of C2H4 oxidation over the TiO2 supported Pt-based monolithic catalysts. The nanoarray catalysts displayed a lower internal mass transfer resistance than the washcoat counterparts as a result of the high macroporosity and small thickness of nanoarray layers. Finally, the nanoarray configuration provides a new pathway towards designing high-performance monolithic reactors and catalysts with low internal diffusion limitations for various gas phase reactions.

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

Cosolvent-tuned interactions in ionic liquids: A vibrational and quantum-chemical study of ethylene glycol ratio effects

Ionic liquids (ILs) are attractive media for CO 2 capture but remain limited by viscosity and cost. Blending ILs with ethylene glycol (EG) is a practical route to mitigate these constraints, yet the molecular origins of cosolvent effects and their dependence on composition are not well resolved. We combine Fourier-transform infrared (FT-IR) spectroscopy with quantum-chemical (DFT) analysis to elucidate how the IL:EG molar ratio modulates intermolecular interactions and electronic structure. Computed vibrational frequencies enable mode assignment and deconvolution of overlapping bands, revealing systematic, ratio-dependent shifts and broadenings in (i) EG O–H stretching, (ii) cation and EG C–H stretchings (imidazolium C2–H, C4–H, C5–H, methyl and ethyl groups, -CH2 of EG), (iii) anion signature modes (e.g., CN motifs), and (iv) EG C–O and C–C stretchings, consistent with the redistribution of hydrogen-bonding networks. Molecular electrostatic potential (MESP) maps quantify attenuation of extreme potential regions with increasing EG, indicating progressive screening of cation–anion electrostatic interactions. Quantum Theory of Atoms in Molecules (QTAIM) identifies emergent bond critical points between EG and the IL ions, while Reduced Density Gradient–Noncovalent Interaction (RDG–NCI) analysis differentiates strong directional hydrogen bonds from dispersive contacts across compositions. Together, these results show that EG fraction controls a switch from predominantly ion–ion to mixed ion–EG coordination, altering local polarity and polarizability that underlie the observed FT-IR trends. The framework provides composition–structure–spectrum relationships that can guide rational selection of IL:EG ratios to balance favorable molecular interactions with practical performance targets in scalable CO 2 capture systems.

DAC↗
DOE OSTI2025

Cobalt(II) Phthalocyanine Substituents Tune the Electrocatalytic CO 2 Conversion to Methanol

Cobalt phthalocyanine (Co(II)Pc) and its derivatives are promising molecular electrocatalysts for the electrochemical reduction of CO 2 to CO and methanol (CH 3 OH). Despite increasing interest, a detailed mechanistic understanding of how ligand substituents influence catalytic activity, selectivity, and efficiency remains limited. In this study, we employ density functional theory (DFT) to systematically investigate the influence of electron-donating groups (EDGs) and electron-withdrawing groups (EWGs) on the electronic structure and redox properties of the Co(II)Pc electrocatalyst, and to elucidate CO 2 RR mechanistic pathways. Our results reveal that EWGs cause a positive shift in the reduction potentials, favor CO 2 binding over protonation of the Co metal center and promote downstream methanol formation at mild potentials. EDGs show opposite trends including favorable protonation steps, promoting a negative shift in the reduction potential, and facilitating the hydrogen evolution reaction (HER), which competes with the desired CO 2 RR pathway. Notably, CO dissociation is thermodynamically and kinetically unfavorable across all systems, positioning the redox potential versus CO dissociation energy as a key factor for methanol selectivity. Furthermore, these insights provide a predictive framework for rational catalyst design and underscore the critical role of electronic tuning in advancing molecular electrocatalysts for sustainable CO 2 conversion.

Alcohols↗
DOE OSTI2024

The Role of Spin–Orbit Coupling in the Linear Absorption Spectrum and Intersystem Crossing Rate Coefficients of Ruthenium Polypyridyl Dyes

The successful use of molecular dyes for solar energy conversion requires efficient charge injection, which in turn requires the formation of states with sufficiently long lifetimes (e.g., triplets). The molecular structure elements that confer this property can be found empirically, however computational predictions using ab initio electronic structure methods are invaluable to identify structure-property relations for dye sensitizers. The primary challenge for simulations to elucidate the electronic and nuclear origins of these properties is a spin-orbit interaction which drives transitions between electronic states. Here, in this work, we present a computational analysis of the spin-orbit corrected linear absorption cross sections and intersystem crossing rate coefficients for a derivative set of phosphonated tris(2,2'-bipyridine)ruthenium(2+) dye molecules. After sampling the ground state vibrational distributions, the predicted linear absorption cross sections indicate that the mixture between singlet and triplet states plays a crucial role in defining the line shape of the metal-to-ligand charge transfer bands in these derivatives. Additionally, an analysis of the intersystem crossing rate coefficients suggests that transitions from the singlet into the triplet manifolds are ultrafast with rate coefficients on the order of 10 13 s -1 for each dye molecule.

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

Molecular Origins of the Barriers to Proton Transport in Acidic Aqueous Solutions

The self-consistent iterative multistate empirical valence bond (SCI-MS-EVB) method is used to analyze the structure, thermodynamics, and dynamics of hydrochloric acid solutions. The reorientation timescales of irreversible proton transport are elucidated by simulating 0.43 M, 0.85 M, 1.68 M, and 3.26 M HCl solutions at 270 K, 285 K, 300 K, 315 K, and 330 K. The results indicate increased counter-ion pairing with increasing concentration, which manifests itself via a reduced hydronium oxygen–chloride (O*-Cl) structuring in the radial distribution functions. Increasing ionic concentration also reduces the diffusion of the hydrated excess protons, principally by reducing the contribution of the Grotthuss proton hopping (shuttling) mechanism to the overall diffusion process. In agreement with prior experimental findings, a decrease in the activation energy of reorientation timescales was also observed, which is explicitly explained using activated rate theory and an energy-entropy decomposition of the state-averaged radial distribution functions. Furthermore, these results provide atomistic verification of suggestions from recent two-dimensional infrared spectroscopy experiments that chloride anions (as opposed to hydrated excess protons) create entropic barriers to proton transport.

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

Promoting Reversible Anionic Redox in Sodium-Ion Cathodes by Doping and Phase Control

Important efforts are underway to harness anionic redox to obtain high-energy Na-ion cathodes. Previously, we identified disruptive dopants in Na–Mn–O that induced reversible oxygen redox. Here, we perform detailed mechanistic studies to understand why these dopants are effective. First, we confirm that no transition metals (TMs) are being oxidized─it is indeed oxygen redox. We also identify that reversible TM migration occurs in the P2 phase where reversible anionic redox occurs, while the migration is irreversible in the distorted P′2 phase. Structural control over the anionic redox is highly significant, but we further elucidate the role of the disruptive dopants. Localized oxygen holes are identified as the source of the reversible anionic redox, and these are deemed to remain stable due to the dopants minimizing the interactions between oxygens to prevent their dimerization. Furthermore, these important contributions to understanding anionic redox will help realize viable high-energy Na-ion batteries.

Impurities↗
DOE OSTI2021

How μ-opioid receptor recognizes fentanyl

Abstract Roughly half of the drug overdose-related deaths in the United States are related to synthetic opioids represented by fentanyl which is a potent agonist of mu-opioid receptor (mOR). In recent years, X-ray crystal structures of mOR in complex with morphine derivatives have been determined; however, structural basis of mOR activation by fentanyl-like opioids remains lacking. Exploiting the X-ray structure of BU72-bound mOR and several molecular simulation techniques, we elucidated the detailed binding mechanism of fentanyl. Surprisingly, in addition to the salt-bridge binding mode common to morphinan opiates, fentanyl can move deeper and form a stable hydrogen bond with the conserved His297 6.52 , which has been suggested to modulate mOR’s ligand affinity and pH dependence by previous mutagenesis experiments. Intriguingly, this secondary binding mode is only accessible when His297 6.52 adopts a neutral HID tautomer. Alternative binding modes may represent a general mechanism in G protein-coupled receptor-ligand recognition.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Human protein synthesis requires aminoacyl-tRNA pivoting during proofreading

Abstract Rigorous studies have characterized the aa-tRNA selection mechanism in bacteria, which is essential for maintaining translational fidelity. Recent investigations have identified critical distinctions in humans, such as the requirement of subunit rolling and a tenfold slower proofreading step. Although these studies captured key intermediates involved in tRNA selection, they did not elucidate the transitions of aa-tRNA between intermediates. Through diverse structure-based simulations, we simulated 1856 aa-tRNA accommodation events into the human ribosomal A site. Here we show the requirement for a distinct ~30° pivoting of aa-tRNA about the anticodon stem within the accommodation corridor. This pivoting is crucial for navigating the crowded accommodation corridor, which becomes more constrained due to subunit rolling. Subunit rolling-dependent crowding increases the steric contributions of the accommodation corridor during aa-tRNA accommodation, consistent with the tenfold reduction in the rate of proofreading. Furthermore, we show that eEF1A interacts with the accommodating aa-tRNA through conserved basic residues, limiting premature aa-tRNA dissociation from the A site. These findings provide a structural description of the human aa-tRNA selection process and demonstrate that the aa-tRNA alignment relative to the ribosomal catalytic sites is a critical determinant of translational fidelity.

Science & Technology - Other Topics↗
DOE OSTI2022

Effect of chemical substitution and external strain on phase stability and ferroelectricity in two dimensional M 2 CT 2 MXenes

Two dimensional ferroelectric materials are gaining increasing attention for use in ultrathin electronic devices owing to the presence of a spontaneous polarization down to one or two monolayers. However, such materials are difficult to identify, especially those with out-of-plane electric polarizations. Previous work predicted that a metastable ferroelectric phase exists in the 2D MXene Sc 2 CO 2 , while further studies have predicted that this phase exists in other MXene chemistries. However, questions remain about the origin of ferroelectricity, the stability of this phase relative to other competing phases, and the effect of external stimuli in these materials. In this work, we use density functional theory calculations to investigate 12 M 2 CT 2 MXenes (M = transition metal, T = surface terminating group) and determine which have the ferroelectric phase as their ground state. We compute these materials’ polarizations, densities of states, phonon band structures, Bader charges, and Born effective charges in the ferroelectric phase to elucidate the reasons for its stabilization. We demonstrate that this ferroelectric phase can be preferentially stabilized in non-ferroelectric MXenes through full chemical substitution of Sc or O, alloying of the Sc sites, or application of epitaxial strain. Finally, we show that these materials have excellent piezoelectric properties as well. This work provides a detailed understanding of ferroelectric MXenes and show how the number of 2D ferroelectric materials can be increased through chemical substitution or application of external stimuli.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Fresnel diffraction imaging of surface nanostructure using coherent resonant x-ray scattering

We investigated surface nanostructures on an antiferromagnet MnBi 2 Te 4 using a novel imaging technique, direct (real)-space and real time coherent x-ray imaging (direct-CXI). This technique has provided new insights into antiferromagnetic textures, including the formation of anti-phase antiferromagnetic (AFM) domains and thermal dynamics of AFM domains and domain walls. While this method produces real-space images of AFM textures without requiring a complex imaging retrieval process, its underlying imaging mechanism has not been fully understood, limiting a deep understanding of AFM textures and the information they contain. By investigating the well-defined structural characteristics of the nanostructures fabricated on MnBi 2 Te 4 ⁠, we elucidate the imaging principle of this novel technique. We find that the observed images can be well explained by the Fresnel diffraction integral. Using a simple model from classical optics, our calculations successfully reproduce the experimentally observed images of the nanostructures. This demonstrates that direct-CXI not only provides straightforward real-space imaging but also contains phase information through its Fresnel diffraction integral.

36 MATERIALS SCIENCE↗
NASA NTRS1993

Study on solidification of immisible alloys (M-10)

Alloying of immiscible alloys under microgravity is of interest in metallurgical processes. Several experiments investigating the alloying of immiscible alloys, such as Al-In, Al-Bi, Zn-Bi, and Zn-Pb, were done in space. Homogeneous distribution of small L2 particles in the matrix, such as an emulsion structure, was expected in the space-solidifed alloys. However, the alloys demonstrated an extremely segregated structure. To date insufficient information was obtained to explain these unexpected results. Our experiment was proposed to clarify the solidification manner of immiscible alloys and to obtain fundamental information concerning structural control of the alloys. In space, density differences between the two liquids separated in immiscible regions can be neglected, so that no sedimentation of L(sub 2) phase will take place. When the growth of the alloys is interrupted and this status is frozen by an adequate rapid cooling procedure, it will provide much information concerning decomposing homogeneous liquid and the interaction between the monotectic growth front morphology and the distribution of L(sub 2) phase. It is anticipated that the results will be useful for elucidating the monotectic solidification manner and it will be instructive to explain the segregated structures obtained in the past space experiments.

Kamio, Akihiko↗
DOE OSTI2021

Long-range structural defects by pathogenic mutations in most severe glucose-6-phosphate dehydrogenase deficiency

Glucose-6-phosphate dehydrogenase (G6PD) deficiency is the most common blood disorder, presenting multiple symptoms, including hemolytic anemia. It affects 400 million people worldwide, with more than 160 single mutations reported in G6PD. The most severe mutations (about 70) are classified as class I, leading to more than 90% loss of activity of the wild-type G6PD. The crystal structure of G6PD reveals these mutations are located away from the active site, concentrating around the noncatalytic NADP + -binding site and the dimer interface. However, the molecular mechanisms of class I mutant dysfunction have remained elusive, hindering the development of efficient therapies. To resolve this, we performed integral structural characterization of five G6PD mutants, including four class I mutants, associated with the noncatalytic NADP + and dimerization, using crystallography, small-angle X-ray scattering (SAXS), cryogenic electron microscopy (cryo-EM), and biophysical analyses. Comparisons with the structure and properties of the wild-type enzyme, together with molecular dynamics simulations, bring forward a universal mechanism for this severe G6PD deficiency due to the class I mutations. We highlight the role of the noncatalytic NADP + -binding site that is crucial for stabilization and ordering two β-strands in the dimer interface, which together communicate these distant structural aberrations to the active site through a network of additional interactions. This understanding elucidates potential paths for drug development targeting G6PD deficiency.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Finite-Temperature Structures of Supported Subnanometer Catalysts Inferred via Statistical Learning and Genetic Algorithm-Based Optimization

Single-atom catalysts (SACs) minimize noble metal utilization and can alter the activity and selectivity of supported metal nanoparticles. However, the morphology of active centers, including single atoms and subnanometer clusters of a few atoms, remains elusive due to experimental challenges. The computational cost to describe numerous cluster shapes and sizes makes direct first-principles calculations impractical. We present a computational framework to enable structure determination for single-atom and subnanometer cluster catalysts. As a case study, we obtained the low energy structures of Pd n (n = 1-21) clusters supported on CeO 2 (111), which are critical components of automobile three-way catalysts. Trained on density functional theory data, a three-dimensional cluster expansion is established using statistical learning to describe the Hamiltonian and predict energies of supported Pdn clusters of any structure. Low energy stable and metastable structures are identified using a Metropolis Monte Carlo-based genetic algorithm in the canonical ensemble at 300 K. We observe that supported single atoms sinter to form bilayer clusters and large cluster isomers share similarities in both shape and energy, and elucidate the significance of the support and microstructure on cluster stability. We discovered a simple surrogate structure-energy model, where the energy per atom scales with the square root of the average first coordination number, which can be used to estimate energies and compare the stability of clusters. Our framework, applicable to any metal/support system, fills an important methodological gap to predict the stability of supported metal catalysts in the subnanometer regime.

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

Structure of the Wnt–Frizzled–LRP6 initiation complex reveals the basis for coreceptor discrimination

Wnt morphogens are critical for embryonic development and tissue regeneration. Canonical Wnts form ternary receptor complexes composed of tissue-specific Frizzled (Fzd) receptors together with the shared LRP5/6 coreceptors to initiate β-catenin signaling. The cryo-EM structure of a ternary initiation complex of an affinity-matured XWnt8–Frizzled8–LRP6 complex elucidates the basis of coreceptor discrimination by canonical Wnts by means of their N termini and linker domains that engage the LRP6 E1E2 domain funnels. Chimeric Wnts bearing modular linker “grafts” were able to transfer LRP6 domain specificity between different Wnts and enable non-canonical Wnt5a to signal through the canonical pathway. Synthetic peptides comprising the linker domain serve as Wnt-specific antagonists. The structure of the ternary complex provides a topological blueprint for the orientation and proximity of Frizzled and LRP6 within the Wnt cell surface signalosome.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Structural coordination between active sites of a CRISPR reverse transcriptase-integrase complex

CRISPR-Cas systems provide adaptive immunity in bacteria and archaea, beginning with integration of foreign sequences into the host CRISPR genomic locus and followed by transcription and maturation of CRISPR RNAs (crRNAs). In some CRISPR systems, a reverse transcriptase (RT) fusion to the Cas1 integrase and Cas6 maturase creates a single protein that enables concerted sequence integration and crRNA production. To elucidate how the RT-integrase organizes distinct enzymatic activities, we present the cryo-EM structure of a Cas6-RT-Cas1—Cas2 CRISPR integrase complex. The structure reveals a heterohexamer in which the RT directly contacts the integrase and maturase domains, suggesting functional coordination between all three active sites. Together with biochemical experiments, our data support a model of sequential enzymatic activities that enable CRISPR sequence acquisition from RNA and DNA substrates. These findings highlight an expanded capacity of some CRISPR systems to acquire diverse sequences that direct CRISPR-mediated interference.

59 BASIC BIOLOGICAL SCIENCES↗