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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 595 records · Page 33
All sourcesNASA NTRSDOE OSTI
DOE OSTI2019

Stimulated X-ray Raman and Absorption Spectroscopy of Iron–Sulfur Dimers

Iron–sulfur complexes play an important role in biological processes such as metabolic electron transport. A detailed understanding of the mechanism of long-range electron transfer requires knowledge of the electronic structure of the complexes, which has traditionally been challenging to obtain, either by theory or by experiment, but the situation has begun to change with advances in quantum chemical methods and intense free electron laser light sources. We compute the spectra for stimulated X-ray Raman spectroscopy (SXRS) and absorption spectroscopy of homovalent and mixed-valence [2Fe–2S] complexes, using the ab initio density matrix renormalization group algorithm. The simulated spectra show clear signatures of the theoretically predicted dense low-lying excited states within the d–d manifold. Finally, the difference in spectral intensity between the absorption-active and Raman-active states provides a potential mechanism to selectively excite states by a proper tuning of the excitation pump, to access the electronic dynamics within this manifold.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Spectroscopic Signature of Proton Location in Proton Bound HSO4-•H+•X- (X = F, Cl, Br, and I) Clusters

Proton transfer plays a vital role in a variety of chemical and biological processes. The proton location in proton bound clusters, specifically, in the anions of HSO4?•H+•X? (X = F, Cl, Br, and I), has been studied by negative ion photoelectron spectroscopy and ab initio theoretical calculations. The measured photoelectron spectra of HSO4?•H+•X? (X = Cl, Br, and I) closely resemble those of X? by simply shifting to higher electron binding energies, suggesting that X? is the chromophore of the electron photodetachment, a fact clearly violating gas-phase acidity predictions. However, in the X = F case, the spectrum of HSO4?•H+•F? is more similar to that of HSO4?, indicating that H+ stays with F? and the HSO4? moiety carries the extra electron. Accompanying theoretical analyses are in excellent agreement with the experimental measurements and observations. This work provides direct spectroscopic evidence of the proton locations, clearly showing cases in which proton affinities of the constituent bases cannot correctly predict the right chemistry involving proton transfer processes.

Hou, Gao-Lei↗
DOE OSTI2017

Multifunctional, Tunable Metal–Organic Framework Materials Platform for Bioimaging Applications [A Multifunctional Tunable MOF Materials Platform for Bio-Imaging Applications]

Herein, we describe a novel multifunctional metal–organic framework (MOF) materials platform that displays both porosity and tunable emission properties as a function of the metal identity (Eu, Nd, and tuned compositions of Nd/Yb). Their emission collectively spans the deep red to near-infrared (NIR) spectral region (~614–1350 nm), which is highly relevant for in vivo bioimaging. These new materials meet important prerequisites as relevant to biological processes: they are minimally toxic to living cells and retain structural integrity in water and phosphate-buffered saline. To assess their viability as optical bioimaging agents, we successfully synthesized the nanoscale Eu analog as a proof-of-concept system in this series. In vitro studies show that it is cell-permeable in individual RAW 264.7 mouse macrophage and HeLa human cervical cancer tissue culture cells. The efficient discrimination between the Eu emission and cell autofluorescence was achieved with hyperspectral confocal fluorescence microscopy, used here for the first time to characterize MOF materials. Importantly, this is the first report that documents the long-term conservation of the intrinsic emission in live cells of a fluorophore-based MOF to date (up to 48 h). As a result this finding, in conjunction with the materials’ very low toxicity, validates the biocompatibility in these systems and qualifies them as promising for use in long-term tracking and biodistribution studies.

36 MATERIALS SCIENCE↗
DOE OSTI2017

Coexistence of Multilayered Phases of Confined Water: The Importance of Flexible Confining Surfaces

Flexible nanoscale confinement is critical to understanding the role that bending fluctuations play on biological processes where soft interfaces are ubiquitous or to exploit confinement effects in engineered systems where inherently flexible 2D materials are pervasively employed. Here, using molecular dynamics simulations, we compare the phase behavior of water confined between flexible and rigid graphene sheets as a function of the in-plane density, ρ2D. We find that both cases show commensurate mono-, bi-, and trilayered states; however, the water phase in those states and the transitions between them are qualitatively different for the rigid and flexible cases. The rigid systems exhibit discontinuous transitions between an ( n )-layer and an ( n +1)-layer state at particular values of ρ2D, whereas under flexible confinement, the graphene sheets bend to accommodate an ( n )-layer and an (n+1)-layer state coexisting in equilibrium at the same density. We show that the flexible walls introduce a very different sequence of ice phases and their phase coexistence with vapor and liquid phases than that observed with rigid walls. We discuss the applicability of these results to real experimental systems to shed light on the role of flexible confinement and its interplay with commensurability effects.

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

General Kinetic Model for pH Dependence of Proton-Coupled Electron Transfer: Application to an Electrochemical Water Oxidation System

The pH dependence of proton-coupled electron transfer (PCET) reactions, which are critical to many chemical and biological processes, is a powerful probe for elucidating their fundamental mechanisms. Herein, a general, multichannel kinetic model is introduced to describe the pH dependence of both homogeneous and electrochemical PCET reactions. According to this model, a weak pH dependence can arise from the competition among multiple sequential and concerted PCET channels involving different forms of the redox species, such as protonated and deprotonated forms, as well as different proton donors and acceptors. The contribution of each channel is influenced by the relative populations of the reactant species, which often depend strongly on pH, leading to complex pH dependence of PCET apparent rate constants. This model is used to explain the origins of the experimentally observed weak pH dependence of the electrochemical PCET apparent rate constant for a ruthenium-based water oxidation catalyst attached to a tin-doped In2O3 (ITO) surface. The weak pH dependence is found to arise from the intrinsic differences in the rate constants of participating channels and the dependence of their relative contributions on pH. This model predicts that the apparent maximum rate constant will become pH-independent at higher pH, which is confirmed by experimental measurements. Our analysis also suggests that the dominant channels are electron transfer at lower pH and sequential PCET via electron transfer followed by fast proton transfer at higher pH. Furthermore, this work highlights the importance of considering multiple competing channels simultaneously for PCET processes.

Catalysts↗
DOE OSTI2025

Sequence Programmable Order–Disorder Transitions in Supramolecular Assembly of Peptide Nanofibers

Protein–protein interactions determine the assembly of complexes that are responsible for numerous key biological processes. The assembly of many natural protein complexes is mediated by post-translational structural changes and environmental stimuli. In this study, we show that incorporation of adjacent lysine residues results in the pH-tunable stability of peptide secondary structure and assembly, allowing for the incorporation of complementary order-inducing motifs. The strategic placement of cysteine pairs in the same peptide sequence results in redox-dependent disulfide staple formation, inducing a transition from random coil to β-sheet conformation and subsequent supramolecular nanofiber assembly from otherwise disordered peptide monomers. Spectroscopic, imaging, molecular dynamics, and kinetic studies highlight the critical role of sequence motif location, oligomerization, and the competitive interplay between intra- and interpeptide disulfide bonding in determining assembly outcomes. We extend this approach to demonstrate phosphorylation-dependent assembly from the design of the same parent peptide sequence, suggesting a general approach to the design of diverse stimulus-responsive peptide sequences for supramolecular assembly. Furthermore, these findings also provide a framework for investigating sequence-dependent pathways in amyloid fiber formation with potential implications for neurodegenerative disease research.

Disulfides↗
DOE OSTI2026

The Factors Governing Metal Dependence of an Emergent Superfamily of Bimetallic Oxygenases

Metalloenzyme superfamilies are typically defined by their protein scaffolds and active sites. Owing to the high tunability of protein structures, members of a single superfamily can catalyze diverse reactions with the same metallocofactor. Some superfamilies, such as amidohydrolase-related dinuclear oxygenases (AROs), display further versatility by utilizing multiple metallocofactors. We have shown that certain AROs catalyze monooxygenation reactions with diiron, dimanganese, and/or mixed manganese−iron cofactors, but the molecular factors governing the selection of a particular cofactor remain unknown, and the extent of this superfamily in biology is unclear. Here, we report bioinformatic analyses that expand the ARO superfamily to approximately 17,000 unique UniProt sequences, far exceeding the number of previously characterized enzymes. Through the integration of structural, spectroscopic, and thermodynamic analyses of representative proteins with a bioinformatic pipeline that identifies key secondary- and tertiary-sphere residues, we can predict in silico the metal preference for the majority of reported ARO sequences. These annotations were validated via the characterization of multiple new AROs, including ones implicated in key oxidative steps of natural product biosyntheses. This study establishes the key structure−function relationships governing metal preferences in AROs and highlights their vastly underappreciated role in myriad biological processes.

Liu, Chang [University of California, Berkeley, CA↗
DOE OSTI2017

Photochemically Generated Thiyl Free Radicals Observed by X-ray Absorption Spectroscopy

Sulfur-based thiyl radicals are known to be involved in a wide range of chemical and biological processes, but they are often highly reactive, which makes them difficult to observe directly. We report herein X-ray absorption spectra and analysis that support the direct observation of two different thiyl species generated photochemically by X-ray irradiation. The thiyl radical sulfur K-edge X-ray absorption spectra of both species are characterized by a uniquely low energy transition at about 2465 eV, which occurs at a lower energy than any previously observed feature at the sulfur K-edge and corresponds to a 1s → 3p transition to the singly occupied molecular orbital of the free radical. In conclusion, our results constitute the first observation of substantial levels of thiyl radicals generated by X-ray irradiation and detected by sulfur K-edge X-ray absorption spectroscopy.

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

Mass Spectrometric Determination of Site-Specific O -Acetylation in Rhamnogalacturonan I Oligomers

O-acetylation, a common modification in rhamnogalacturonan I (RG-I), is critical for various biological processes, including plant growth, stress responses, and pathogen defense. Precise determination of the degree and specific positions of acetylation is therefore essential. To date, nuclear magnetic resonance (NMR) and tandem mass spectrometry have been employed to identify O-acetyl positions in pectin oligosaccharides. Although NMR is effective, it requires pure, high-concentration samples. Tandem mass spectrometry (MS), which uses smaller sample amounts, faces challenges due to O-acetyl migration between monosaccharide positions. The multiple steps in pectin sample analysis can further promote O-acetyl migration, especially near free hydroxyl groups. Moreover, during tandem MS, O-acetyl groups may detach, complicating the accurate tracking. This study presents an approach to lock O-acetyl groups by introducing trideuteroacetyl and propionyl substituents onto free hydroxyls of RG-I or partially acetylated RG-I. By combining matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) MS and electrospray ionization (ESI) MS with MS/MS or tandem mass spectrometry (MSn), we devised a way to determine the monosaccharide sequence in the oligomer and the precise positions of O-acetyl groups in partially acetylated RG-I. This method enables the study of the regiospecificity of recombinant pectin O-acetyltransferases and can be applied to other oligosaccharides to determine acyl positions.

O-acetylation↗
DOE OSTI2019

Initiation and Development of Wetlands in Southern Florida Karst Landscape Associated With Accumulation of Organic Matter and Vegetation Evolution

Biological processes can exert important controls on geomorphic evolution in karst landscapes, because carbonate mineral dissolution is augmented and spatially focused by the production of CO 2 and biogenic acids from organic matter (OM) decomposition. In Big Cypress National Preserve (BICY) in southwest Florida (USA), depressional wetlands embedded in a mosaic of pine uplands exhibit regular patterning. To understand the impact of OM decomposition as well as different OM sources on carbonate dissolution and landscape patterning, we measured bulk OM property and biomarker proxies (fatty acids and lignin phenols) in different zones (center vs. edge) of the depressional wetlands. We also constructed age profiles of sediment accretion and pattern genesis using 210Pb activities and compound- specific radiocarbon analysis (CSRA) of long-chain fatty acids. Bulk OM and biomarker data indicate rapid OM accumulation in wetland centers resulting from high primary production and near permanent inundation, in contrast to negligible OM accumulation at wetland edges. Age discontinuities suggest episodic periods of near complete OM loss due to decomposition and/or fire. Based on CSRA, landscape patterning likely initiated in the mid-to-late Holocene, with wetlands at slight higher elevation initiated earlier than wetlands at lower elevation. Bulk stable isotope and lignin phenol biomarkers indicate wetland vegetation was initially dominated by herbaceous species and shifted to woody dominated vegetation as landscape hydrology adjusted to changing precipitation. The rate of weathering is likely impacted by hydrological conditions, vegetation dynamics and environmental perturbations like precipitation and fires, suggesting that this karst landscape is a manifestation of complex ecosystem feedbacks.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2019

Leveraging Environmental Research and Observation Networks to Advance Soil Carbon Science

Soil organic matter (SOM) is a critical ecosystem variable regulated by interacting physical, chemical, and biological processes. Collaborative efforts to integrate perspectives, data, and models from interdisciplinary research and observation networks can significantly advance predictive understanding of SOM. We outline how integrating three networks—the Long-Term Ecological Research with a focus on ecological dynamics, the Critical Zone Observatories with strengths in landscape/geologic context, and the National Ecological Observatory Network with standardized multiscale measurements—can advance SOM knowledge. This integration requires improved data dissemination and sharing, coordinated data collection activities, and enhanced collaboration between empiricists and modelers within and across networks.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Structural Uncertainty in the Sensitivity of Urban Temperatures to Anthropogenic Heat Flux

One key source of uncertainty for weather and climate models is structural uncertainty arising from the fact that these models must simplify or approximate complex physical, chemical, and biological processes that occur in the real world. However, structural uncertainty is rarely examined in the context of simulated effects of anthropogenic heat flux in cities. Using the Weather Research and Forecasting (WRF) model coupled with a single-layer urban canopy model, it is found that the sensitivity of urban canopy air temperature to anthropogenic heat flux can differ by an order of magnitude depending on how anthropogenic heat flux is released to the urban environment. Moreover, varying model structures through changing the treatment of roof-air interaction and the parameterization of convective heat transfer between the canopy air and the atmosphere can affect the sensitivity of urban canopy air temperature by a factor of 4. Urban surface temperature and 2-m air temperature are less sensitive to the methods of anthropogenic heat flux release and the examined model structural variants than urban canopy air temperature, but their sensitivities to anthropogenic heat flux can still vary by as much as a factor of 4 for surface temperature and 2 for 2-m air temperature. Our study recommends using temperature sensitivity instead of temperature response to understand how various physical processes (and their representations in numerical models) modulate the simulated effects of anthropogenic heat flux.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2017

Polycomb-like proteins link the PRC2 complex to CpG islands

The Polycomb repressive complex 2 (PRC2) mainly mediates transcriptional repression1,2 and has essential roles in various biological processes including the maintenance of cell identity and proper differentiation. Polycomb-like (PCL) proteins, such as PHF1, MTF2 and PHF19, are PRC2-associated factors that form sub-complexes with PRC2 core components3, and have been proposed to modulate the enzymatic activity of PRC2 or the recruitment of PRC2 to specific genomic loci4,5,6,7,8,9,10,11,12,13. Mammalian PRC2-binding sites are enriched in CG content, which correlates with CpG islands that display a low level of DNA methylation14. However, the mechanism of PRC2 recruitment to CpG islands is not fully understood. Here we solve the crystal structures of the N-terminal domains of PHF1 and MTF2 with bound CpG-containing DNAs in the presence of H3K36me3-containing histone peptides. We show that the extended homologous regions of both proteins fold into a winged-helix structure, which specifically binds to the unmethylated CpG motif but in a completely different manner from the canonical winged-helix DNA recognition motif. We also show that the PCL extended homologous domains are required for efficient recruitment of PRC2 to CpG island-containing promoters in mouse embryonic stem cells. Our research provides the first, to our knowledge, direct evidence to demonstrate that PCL proteins are crucial for PRC2 recruitment to CpG islands, and further clarifies the roles of these proteins in transcriptional regulation in vivo.

58 GEOSCIENCES↗
DOE OSTI2017

Nanoscale π–π stacked molecules are bound by collective charge fluctuations

Non-covalent π-π interactions are central to chemical and biological processes, yet the full understanding of their origin that would unite the simplicity of empirical approaches with the accuracy of quantum calculations is still missing. Here we employ a quantum-mechanical Hamiltonian model for van der Waals interactions, to demonstrate that intermolecular electron correlation in large supramolecular complexes at equilibrium distances is appropriately described by collective charge fluctuations. We visualize these fluctuations and provide connections both to orbital-based approaches to electron correlation, as well as to the simple London pairwise picture. The reported binding energies of ten supramolecular complexes obtained from the quantum-mechanical fluctuation model joined with density functional calculations are within 5% of the reference energies calculated with the diffusion quantum Monte-Carlo method. Our analysis suggests that π-π stacking in supramolecular complexes can be characterized by strong contributions to the binding energy from delocalized, collective charge fluctuations—in contrast to complexes with other types of bonding.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2017

Modulating supramolecular binding of carbon dioxide in a redox-active porous metal-organic framework

Hydrogen bonds dominate many chemical and biological processes, and chemical modification enables control and modulation of host–guest systems. Here in this paper we report a targeted modification of hydrogen bonding and its effect on guest binding in redox-active materials. MFM-300(V III ) {[V III 2 (OH) 2 (L)], LH 4 =biphenyl-3,3',5,5'-tetracarboxylic acid} can be oxidized to isostructural MFM-300(V IV ), [V IV 2 O 2 (L)], in which deprotonation of the bridging hydroxyl groups occurs. MFM-300(V III ) shows the second highest CO 2 uptake capacity in metal-organic framework materials at 298 K and 1 bar (6.0 mmol g -1 ) and involves hydrogen bonding between the OH group of the host and the O-donor of CO 2 , which binds in an end-on manner, OH∙∙∙ =1.863(1) Å. In contrast, CO 2 -loaded MFM-300(V IV ) shows CO 2 bound side-on to the oxy group and sandwiched between two phenyl groups involving a unique O CO$_2$ ···c.g.phenyl interaction [3.069(2), 3.146(3) Å]. Lastly, the macroscopic packing of CO 2 in the pores is directly influenced by these primary binding sites.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2017

Large sulfur isotope fractionations in Martian sediments at Gale crater

Variability in the sulfur isotopic composition in sediments can reflect atmospheric, geologic and biological processes. Evidence for ancient fluvio-lacustrine environments at Gale crater on Mars and a lack of efficient crustal recycling mechanisms on the planet suggests a surface environment that was once warm enough to allow the presence of liquid water, at least for discrete periods of time, and implies a greenhouse effect that may have been influenced by sulfur-bearing volcanic gases. Here we report in situ analyses of the sulfur isotopic compositions of SO 2 volatilized from ten sediment samples acquired by NASA's Curiosity rover along a 13 km traverse of Gale crater. We find large variations in sulfur isotopic composition that exceed those measured for Martian meteorites and show both depletion and enrichment in34S. Measured values of δ 34 S range from - 47 ± 14‰ to 28 ± 7‰, similar to the range typical of terrestrial environments. Although limited geochronological constraints on the stratigraphy traversed by Curiosity are available, we propose that the observed sulfur isotopic signatures at Gale crater can be explained by equilibrium fractionation between sulfate and sulfide in an impact-driven hydrothermal system and atmospheric processing of sulfur-bearing gases during transient warm periods.

58 GEOSCIENCES↗
DOE OSTI2022

Observation of site-selective chemical bond changes via ultrafast chemical shifts

The concomitant motion of electrons and nuclei on the femtosecond time scale marks the fate of chemical and biological processes. Here we demonstrate the ability to initiate and track the ultrafast electron rearrangement and chemical bond breaking site-specifically in real time for the carbon monoxide diatomic molecule. We employ a local resonant x-ray pump at the oxygen atom and probe the chemical shifts of the carbon core-electron binding energy. We observe charge redistribution accompanying core-excitation followed by Auger decay, eventually leading to dissociation and hole trapping at one site of the molecule. The presented technique is general in nature with sensitivity to chemical environment changes including transient electronic excited state dynamics. This work provides a route to investigate energy and charge transport processes in more complex systems by tracking selective chemical bond changes on their natural timescale.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Unraveling iron oxides as abiotic catalysts of organic phosphorus recycling in soil and sediment matrices

In biogeochemical phosphorus cycling, iron oxide minerals are acknowledged as strong adsorbents of inorganic and organic phosphorus. Dephosphorylation of organic phosphorus is attributed only to biological processes, but iron oxides could also catalyze this reaction. Evidence of this abiotic catalysis has relied on monitoring products in solution, thereby ignoring iron oxides as both catalysts and adsorbents. Here we apply high-resolution mass spectrometry and X-ray absorption spectroscopy to characterize dissolved and particulate phosphorus species, respectively. In soil and sediment samples reacted with ribonucleotides, we uncover the abiotic production of particulate inorganic phosphate associated specifically with iron oxides. Reactions of various organic phosphorus compounds with the different minerals identified in the environmental samples reveal up to twenty-fold greater catalytic reactivities with iron oxides than with silicate and aluminosilicate minerals. Importantly, accounting for inorganic phosphate both in solution and mineral-bound, the dephosphorylation rates of iron oxides were within reported enzymatic rates in soils. Our findings thus imply a missing abiotic axiom for organic phosphorus mineralization in phosphorus cycling.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗