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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 37 records · Page 2
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Molecular Dynamical and Quantum Mechanical Exploration of the Site-Specific Dynamics of Cy3 Dimers Internally Linked to dsDNA

Performing spectroscopic measurements on biomolecules labeled with fluorescent probes is a powerful approach to locating the molecular behavior and dynamics of large systems at specific sites within their local environments. The indocarbocyanine dye Cy3 has emerged as one of the most commonly used chromophores. The incorporation of Cy3 dimers into DNA enhances experimental resolution owing to the spectral characteristics influenced by the geometric orientation of excitonically coupled monomeric units. Various theoretical models and simulations have been utilized to aid in the interpretation of the experimental spectra. In this study, we employ all-atom molecular dynamics simulations to study the structural dynamics of Cy3 dimers internally linked to the dsDNA backbone. We used quantum mechanical calculations to derive insights from both the linear absorption spectra and the circular dichroism data. Furthermore, we explore potential limitations within a commonly used force field for cyanine dyes. The molecular dynamics simulations suggest the presence of four possible Cy3 dimeric populations. The spectral simulations on the four populations show one of them to agree better with the experimental signatures, suggesting it to be the dominant population. Furthermore, the relative orientation of Cy3 in this population compares very well with previous predictions from the Holstein–Frenkel Hamiltonian model.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Specific Ion Effects in Lanthanide–Amphiphile Structures at the Air–Water Interface and Their Implications for Selective Separation

The use of surfactants to attract dissolved ions to water surfaces and interfaces is an essential step in both solvent-based and solvent-free separation processes. Here, we have studied the interactions of lanthanide ions in the aqueous subphase with monolayers of dihexadecyl phosphate at air–water interfaces. With heavier lanthanides (atomic number Z ≥ 65) in the subphase, the floating layer can be compressed to an area/molecule of about half the molecular cross section, indicating bilayer formation. X-ray fluorescence and reflectivity data support this conclusion. In the presence of lighter lanthanides (Z < 65), only monolayers are observed. Subphase-concentration-dependent studies using Er 3+ (heavier) and Nd 3+ (lighter) lanthanides show a stepwise progression, with ions attaching to the monolayer only when the solution concentration is >3 × 10 –7 M. Above ~10 –5 M, bilayers form but only in the presence of the heavier lanthanide. Grazing incidence X-ray diffraction shows evidence of lateral ion–ion correlations in the bilayer structure but not in monolayers. Explicit solvent all-atom molecular dynamics simulations confirm the elevated ion–ion correlation in the bilayer system. This bilayer structure isolates heavier lanthanides but not lighter lanthanides from an aqueous solution and is therefore a potential mechanism for the selective separation of heavier lanthanides.

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

Recommendations for improving rigor and reproducibility in site specific characterization

Heterogeneous catalysis is driven by the interaction of reactant molecules and the catalyst surface. The locus of this interaction as well as the surrounding ensemble of atoms is referred to as the catalyst active site. Active site characterization attempts to distinguish active catalytic sites from inactive surface sites, to elucidate the structural and chemical nature of active sites, and to quantify active site concentration. Numerous techniques have been demonstrated to provide compositional and structural information about the active sites within a catalyst. However, each technique has its own limitations and experimental pitfalls that can lead to data misinterpretation or irreproducible results. Further, this work aims to provide an overview of the types of data that can be collected, to outline common experimental challenges and how to avoid them, and to assemble relevant references for the most used active site characterization techniques. More broadly, we aim to outline best practices for researchers to collect, interpret, and report active site characterization data in a way that provides the most benefit to the broader catalysis community. Increasing the rigor and reproducibility of active site characterization offers a strategy to better link properties with catalytic performance and to enable the community to develop consensus concerning these relationships.

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

Specific iron binding to natural sphingomyelin membrane induced by non-specific co-solutes

Sphingomyelin (SPM), a crucial phospholipid in the myelin sheath, plays a vital role in insulating nerve fibers. We hypothesize that iron ions selectively bind to the phosphatidylcholine (PC) template within the SPM membrane under near-physiological conditions, resulting in disruptions to membrane organization. These interactions could potentially contribute to the degradation of the myelin sheath, thereby playing a role in the development of neurodegenerative diseases. We utilized synchrotron-based X-ray spectroscopy and diffraction techniques to study the interaction of iron ions with a bovine spinal-cord SPM monolayer (ML) at the liquid-vapor interface under physiological conditions. The SPM ML serves as a model system, representing localized patches of lipids within a more complex membrane structure. The experiments assessed iron binding to the SPM membrane both in the presence of salts and with additional evaluation of the effects of various ion species on membrane behavior. Grazing incidence X-ray diffraction was employed to analyze the impact of iron binding on the structural integrity of the SPM membrane. Furthermore, our results demonstrate that iron ions in dilute solution selectively bind to the PC template of the SPM membrane exclusively at near-physiological salt concentrations (e.g., NaCl, KCl, KI, or CaCl 2 ) and are pH-dependent. In-significant binding was detected in the absence of these salts or at near-neutral pH with salts. The surface adsorption of iron ions is correlated with salt concentration, reaching saturation at physiological levels. In contrast, multivalent ions such as La 3+ and Ca 2+ do not bind to SPM under similar conditions. Notably, iron binding to the SPM membrane disrupts its in-plane organization, suggesting that these interactions may compromise membrane integrity and contribute to myelin sheath damage associated with neurological disorders.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Mapping the Temperature-dependent and network site-specific onset of spectral diffusion at the surface of a water cluster cage

We explore the kinetic processes that sustain equilibrium in a microscopic, finite system. This is accomplished by monitoring the spontaneous, time-dependent frequency evolution (the frequency autocorrelation) of a single OH oscillator, embedded in a water cluster held in a temperature-controlled ion trap. The measurements are carried out by applying two-color, IR-IR photodissociation mass spectrometry to the D3O+?(HDO)(D2O)19 isotopologue of the “magic number” protonated water cluster, H+?(H2O)21. The OH group can occupy any one of the five spectroscopically distinct sites in the distorted pentagonal dodecahedron cage structure. The OH frequency is observed to evolve over tens of milliseconds in the temperature range (90-120 K). Starting at 100 K, large “jumps” are observed between two OH frequencies separated by ~300 cm-1 indicating migration of the OH group from the bound OH site at 3350 cm-1 to the free position at 3686 cm-1. Increasing the temperature to 110 K leads to partial interconversion among many sites. All sites are observed to interconvert at 120 K such that the distribution of the unique OH group among them adopts the form one would expect for a canonical ensemble. The spectral dynamics displayed by the clusters thus offer an unprecedented view into the molecular-level processes that drive spectral diffusion in an extended network of water molecules.

Yang, Nan↗
DOE OSTI2022

Interannual consistency of migration phenology is season- and breeding region-specific in North American Golden Eagles

Abstract Interannual consistency (an indicator of the strength of adjustments) in migration phenology of Golden Eagles (Aquila chrysaetos) in North America is most strongly associated with the breeding region, the season, and with late-season temperature on breeding and wintering grounds. Consistency was greatest in boreal spring migration and the breeding regions of eastern Canada. Using multi-year GPS tracks of 83 adults breeding in 3 spatially distant regions (Alaska, northeast Canada, and southeast Canada), we quantified the interannual consistency of migration phenology and wintering latitude within and among individuals tracked across multiple years and the repeatability (r) by breeding regions and seasons. By comparing regions and seasons, we found that consistency was highest (r > 0.85) for boreal spring migration in eastern Canada while Alaska had the lowest value (r < 0.15). Because seasonal consistency of migration phenology was only detected in eastern Canada, we conclude that seasonal features are not a primary constraint. While regional differences in consistency were not related to differences in migratory distances, they could be the result of genetic or habitat differences. We also found that temperatures warmer than the decadal average at the region of departure delayed the start of boreal spring migration by ~10 days and advanced boreal autumn migration by ~20 days. These results suggest that warmer temperatures would reduce residence time on breeding grounds, contrary to expectations and trends found in other studies. Wide variations in migratory strategies across a species distribution can add to the list of challenges for conservation but may give migrants the capacity to acclimate to environmental changes.

Zoology↗