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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 559 records · Page 31
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 OSTI2016

Impacts of Surface Site Coordination on Arsenate Adsorption: Macroscopic Uptake and Binding Mechanisms on Aluminum Hydroxide Surfaces

Aluminum hydroxides play important roles in regulating the fate and transport of contaminants and nutrients in soils and aquatic systems. Like many metal oxides, these minerals display surface functional groups in a series of coordination states, each of which may differ in its affinity for adsorbates. The distribution of functional group types varies among distinct surfaces of aluminum hydroxides, and we thus hypothesize that the adsorption behavior and mechanisms will show a dependence on particle morphology. To test this hypothesis, we investigate arsenate adsorption on two aluminum hydroxide polymorphs with distinct particle morphologies, gibbsite [γ-Al(OH) 3 ] and bayerite [α-Al(OH) 3 ], at pH 4 and 7. Synthetic gibbsite platelets expose large (001) basal surfaces predicted to be terminated by doubly coordinated functional groups (>Al 2 OH). In contrast, synthetic bayerite microrods display mainly edge surfaces (parallel to the c axis) containing abundant singly coordinated functional groups (>AlOH 2 ). Macroscopic adsorption studies show that gibbsite adsorbs less arsenate per unit surface area than bayerite at both pH values and suggest that two surface complexes form on each material. Similar electrokinetic behavior is displayed at the same relative coverages of arsenate, suggesting that similar reactive surface groups (>AlOH 2 ) control the surface charging on both particles. EXAFS spectroscopy shows that there is no variation in arsenate surface speciation on a given mineral with surface coverage or pH. Whereas bidentate binuclear inner-sphere species are the dominant complexes present, the EXAFS result suggest that outer-sphere species also occur on both minerals, with a greater abundance on gibbsite. This binding mode likely involves adsorption to >Al 2 OH sites, which have a slow ligand exchange rate that inhibits inner-sphere binding. Lastly, these results demonstrate that adsorption mechanisms and capacity, even when normalized for specific surface area, vary with metal oxide particle morphology because of the distribution of distinct functional groups.

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

Ammonia-Assisted Light Alkane Anti-coke Reforming on Isolated ReO x Sites in Zeolite

The conventional reforming produces H 2 with stoichiometric amounts of CO and CO 2 from hydrocarbons. Here, we show that CO x -free H 2 can be produced from ammonia-assisted reforming (ammoreforming) of natural gas liquids (C n H 2n+2 + nNH 3 = nHCN + (2n + 1) H 2 , n = 2 or 3) at the same conditions as the steam reforming. Such a process co-produces HCN, which can be easily separated from H 2 and used as value-added chemicals or for NH 3 recycling through hydrolysis. In addition, the ammoreforming of ethane and propane was realized over the Re-modified HZSM-5 zeolite rather than the traditional Pt-based catalyst for the BMA process (methane ammoreforming). The specific activity of the Re/HZSM-5 catalysts at 650 °C is up to 1 mol H2 /g Re /min (or 180 min –1 ) during ethane ammoreforming. The catalyst is highly coke resistant and shows only slight deactivation with a time-on-stream up to 20 h. Characterization of the fresh and used catalysts by X-ray absorption and Raman spectroscopies suggested that the isolated ReO x site grafted by AlO 4 – tetrahedral in the zeolite framework is responsible for the outstanding catalytic activity and coke resistibility.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2012

Gold-Copper Nanoparticles: Nanostructural Evolution and Bifunctional Catalytic Sites

Understanding of the atomic-scale structure is essential for exploiting the unique catalytic properties of any nanoalloy catalyst. This report describes novel findings of an investigation of the nanoscale alloying of gold-copper (AuCu) nanoparticles and its impact on the surface catalytic functions. Two pathways have been explored for the formation of AuCu nanoparticles of different compositons, including wet chemical synthesis from mixed Au- and Cu-precursor molecules, and nanoscale alloying via an evolution of mixed Au- and Cu-precursor nanoparticles near the nanoscale melting temperatures. For the evolution of mixed precursor nanoparticles, synchrotron x-ray based in-situ real time XRD was used to monitor the structural changes, revealing nanoscale alloying and reshaping towards an fcc-type nanoalloy (particle or cube) via a partial melting–resolidification mechanism. The nanoalloys supported on carbon or silica were characterized by in-situ high-energy XRD/PDFs, revealing an intriguing lattice "expanding-shrinking" phenomenon depending on whether the catalyst is thermochemically processed under oxidative or reductive atmosphere. This type of controllable structural changes is found to play an important role in determining the catalytic activity of the catalysts for carbon monoxide oxidation reaction. The tunable catalytic activities of the nanoalloys under thermochemically oxidative and reductive atmospheres are also discussed in terms of the bifunctional sites and the surface oxygenated metal species for carbon monoxide and oxygen activation.

Environmental Molecular Sciences Laboratory↗
DOE OSTI2022

Molecular basis for cooperative binding and synergy of ATP-site and allosteric EGFR inhibitors

Abstract Lung cancer is frequently caused by activating mutations in the epidermal growth factor receptor (EGFR). Allosteric EGFR inhibitors offer promise as the next generation of therapeutics, as they are unaffected by common ATP-site resistance mutations and synergize with the drug osimertinib. Here, we examine combinations of ATP-competitive and allosteric inhibitors to better understand the molecular basis for synergy. We identify a subset of irreversible EGFR inhibitors that display positive binding cooperativity and synergy with the allosteric inhibitor JBJ-04-125-02 in several EGFR variants. Structural analysis of these complexes reveals conformational changes occur mainly in the phosphate-binding loop (P-loop). Mutation of F723 in the P-loop reduces cooperative binding and synergy, supporting a mechanism in which F723-mediated contacts between the P-loop and the allosteric inhibitor are critical for synergy. These structural and mechanistic insights will aid in the identification and development of additional inhibitor combinations with potential clinical value.

Beyett, Tyler S. (ORCID:0000000155097004)↗
DOE OSTI2022

Rapid atom-efficient polyolefin plastics hydrogenolysis mediated by a well-defined single-site electrophilic/cationic organo-zirconium catalyst

Polyolefins comprise a major fraction of single-use plastics, yet their catalytic deconstruction/recycling has proven challenging due to their inert saturated hydrocarbon connectivities. Here a very electrophilic, formally cationic earth-abundant single-site organozirconium catalyst chemisorbed on a highly Brønsted acidic sulfated alumina support and characterized by a broad array of experimental and theoretical techniques, is shown to mediate the rapid hydrogenolytic cleavage of molecular and macromolecular saturated hydrocarbons under mild conditions, with catalytic onset as low as 90 °C/0.5 atm H 2 with 0.02 mol% catalyst loading. For polyethylene, quantitative hydrogenolysis to light hydrocarbons proceeds within 48 min with an activity of > 4000 mol(CH 2 units)·mol(Zr) –1 ·h –1 at 200 °C/2 atm H 2 pressure. Under similar solventless conditions, polyethylene-co–1-octene, isotactic polypropylene, and a post-consumer food container cap are rapidly hydrogenolyzed to low molecular mass hydrocarbons. Regarding mechanism, theory and experiment identify a turnover-limiting C-C scission pathway involving ß-alkyl transfer rather than the more common σ-bond metathesis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

Communication: Active space decomposition with multiple sites: Density matrix renormalization group algorithm

We extend the active space decomposition method, recently developed by us, to more than two active sites using the density matrix renormalization group algorithm. The fragment wave functions are described by complete or restricted active-space wave functions. Numerical results are shown on a benzene pentamer and a perylene diimide trimer. It is found that the truncation errors in our method decrease almost exponentially with respect to the number of renormalization states M, allowing for numerically exact calculations (to a few μE{sub h} or less) with M = 128 in both cases. This rapid convergence is because the renormalization steps are used only for the interfragment electron correlation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2016

Transcription of lncRNA prt , clustered prt RNA sites for Mmi1 binding, and RNA polymerase II CTD phospho-sites govern the repression of pho1 gene expression under phosphate-replete conditions in fission yeast

Expression of fission yeast Pho1 acid phosphatase is repressed during growth in phosphate-rich medium. Repression is mediated by transcription of the prt locus upstream of pho1 to produce a long noncoding (lnc) prt RNA. Repression is also governed by RNA polymerase II CTD phosphorylation status, whereby inability to place a Ser7-PO 4 mark (as in S7A) derepresses Pho1 expression, and inability to place a Thr4-PO 4 mark (as in T4A) hyper-represses Pho1 in phosphate replete cells. Here we find that basal pho1 expression from the prt–pho1 locus is inversely correlated with the activity of the prt promoter, which resides in a 110-nucleotide DNA segment preceding the prt transcription start site. CTD mutations S7A and T4A had no effect on the activity of the prt promoter or the pho1 promoter, suggesting that S7A and T4A affect post-initiation events in prt lncRNA synthesis that make it less and more repressive of pho1, respectively. prt lncRNA contains clusters of DSR (determinant of selective removal) sequences recognized by the YTH-domain-containing protein Mmi1. Altering the nucleobase sequence of two DSR clusters in the prt lncRNA caused hyper-repression of pho1 in phosphate replete cells, concomitant with increased levels of the prt transcript. The isolated Mmi1 YTH domain binds to RNAs with single or tandem DSR elements, to the latter in a noncooperative fashion. We report the 1.75 Å crystal structure of the Mmi1 YTH domain and provide evidence that Mmi1 recognizes DSR RNA via a binding mode distinct from that of structurally homologous YTH proteins that recognize m 6 A-modified RNA.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2012

Comments on Resident Farmer DCGLS for Site Soils at the Curtiss-Wright Site in Cheswick, Pennsylvania DCN: 5000-TR-04-0

Oak Ridge Associated Universities (ORAU), via the Oak Ridge Institute for Science and Education contract, evaluated the Enercon Services, Inc. report on site soils derived concentration guideline levels (DCGLs). The RESRAD code Version 6.5 was used in deterministic mode to consider a range of radionuclides and potential future receptors. A standard sensitivity analysis was also included, along with a probabilistic analysis to select conservative input values for the most sensitive physical parameters.

54 ENVIRONMENTAL SCIENCES↗