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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 919 records · Page 51
All sourcesNASA NTRSDOE OSTI
DOE OSTI2012

Structure of a Specialized Acyl Carrier Protein Essential for Lipid A Biosynthesis with Very Long-chain Fatty Acids in Open and Closed Conformations

The solution nuclear magnetic resonance (NMR) structures and backbone (15)N dynamics of the specialized acyl carrier protein (ACP), RpAcpXL, from Rhodopseudomonas palustris, in both the apo form and holo form modified by covalent attachment of 4'-phosphopantetheine at S37, are virtually identical, monomeric, and correspond to the closed conformation. The structures have an extra α-helix compared to the archetypical ACP from Escherichia coli, which has four helices, resulting in a larger opening to the hydrophobic cavity. Chemical shift differences between apo- and holo-RpAcpXL indicated some differences in the hinge region between α2 and α3 and in the hydrophobic cavity environment, but corresponding changes in nuclear Overhauser effect cross-peak patterns were not detected. In contrast to the NMR structures, apo-RpAcpXL was observed in an open conformation in crystals that diffracted to 2.0 Å resolution, which resulted from movement of α3. On the basis of the crystal structure, the predicted biological assembly is a homodimer. Although the possible biological significance of dimerization is unknown, there is potential that the resulting large shared hydrophobic cavity could accommodate the very long-chain fatty acid (28-30 carbons) that this specialized ACP is known to synthesize and transfer to lipid A. These structures are the first representatives of the AcpXL family and the first to indicate that dimerization may be important for the function of these specialized ACPs.

Environmental Molecular Sciences Laboratory↗
DOE OSTI2012

Synthesis, Structure, and Metalation of Two New Highly Porous Zirconium Metal-Organic Frameworks

Three new metal-organic frameworks [MOF-525, Zr 6 O 4 (OH) 4 (TCPP-H 2 ) 3 ; MOF-535, Zr 6 O 4 (OH) 4 (XF) 3 ; MOF-545, Zr 6 O 8 (H 2 O) 8 (TCPP-H 2 ) 2 , where porphyrin H 4 -TCPP-H 2 = (C 48 H 24 O 8 N 4 ) and cruciform H 4 -XF = (C 42 O 8 H 22 )] based on two new topologies, ftw and csq, have been synthesized and structurally characterized. MOF-525 and -535 are composed of Zr 6 O 4 (OH) 4 cuboctahedral units linked by either porphyrin (MOF-525) or cruciform (MOF-535). Another zirconium-containing unit, Zr 6 O 8 (H 2 O) 8 , is linked by porphyrin to give the MOF-545 structure. The structure of MOF-525 was obtained by analysis of powder X-ray diffraction data. The structures of MOF-535 and -545 were resolved from synchrotron single-crystal data. MOF-525, -535, and -545 have Brunauer-Emmett-Teller surface areas of 2620, 1120, and 2260 m 2 /g, respectively. In addition to their large surface areas, both porphyrin-containing MOFs are exceptionally chemically stable, maintaining their structures under aqueous and organic conditions. MOF-525 and -545 were metalated with iron(III) and copper(II) to yield the metalated analogues without losing their high surface area and chemical stability.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Crystal structure of rhodopsin bound to arrestin by femtosecond X-ray laser

G-protein-coupled receptors (GPCRs) signal primarily through G proteins or arrestins. Arrestin binding to GPCRs blocks G protein interaction and redirects signalling to numerous G-protein-independent pathways. Here we report the crystal structure of a constitutively active form of human rhodopsin bound to a pre-activated form of the mouse visual arrestin, determined by serial femtosecond X-ray laser crystallography. Together with extensive biochemical and mutagenesis data, the structure reveals an overall architecture of the rhodopsin-arrestin assembly in which rhodopsin uses distinct structural elements, including transmembrane helix 7 and helix 8, to recruit arrestin. Correspondingly, arrestin adopts the pre-activated conformation, with a ~20° rotation between the amino and carboxy domains, which opens up a cleft in arrestin to accommodate a short helix formed by the second intracellular loop of rhodopsin. In conclusion, this structure provides a basis for understanding GPCR-mediated arrestin-biased signalling and demonstrates the power of X-ray lasers for advancing the frontiers of structural biology.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2018

Topologically guided tuning of Zr-MOF pore structures for highly selective separation of C6 alkane isomers

Effective separation of alkane isomers is a critical step in the petroleum refining process to produce gasoline with high octane rating. Current technology relies on energy intensive distillation method. Adsorptive separation using porous solids offers an alternative route that is more cost effective, lower energy and higher efficiency. Guided by topology-directed design and synthesis, we have developed a series of zirconium-based metal-organic frameworks with optimized pore structure for efficient separation of C6 alkane isomers, Zr-bptc adsorbs a large amount of n-hexane while excluding branched isomers. The n-hexane uptake is ~70% higher than that of a benchmark adsorbent, zeolite-5A. A derivative structure, Zr-abtc, is capable of discriminating all three C6 isomers with a high separation factor for 3-methylpentane over 2,3-dimethylbutane. This property is important for producing gasoline with further improved quality.

36 MATERIALS SCIENCE↗
DOE OSTI2019

Structural water and disordered structure promote aqueous sodium-ion energy storage in sodium-birnessite

Abstract Birnessite is a low-cost and environmentally friendly layered material for aqueous electrochemical energy storage; however, its storage capacity is poor due to its narrow potential window in aqueous electrolyte and low redox activity. Herein we report a sodium rich disordered birnessite (Na 0.27 MnO 2 ) for aqueous sodium-ion electrochemical storage with a much-enhanced capacity and cycling life (83 mAh g −1 after 5000 cycles in full-cell). Neutron total scattering and in situ X-ray diffraction measurements show that both structural water and the Na-rich disordered structure contribute to the improved electrochemical performance of current cathode material. Particularly, the co-deintercalation of the hydrated water and sodium-ion during the high potential charging process results in the shrinkage of interlayer distance and thus stabilizes the layered structure. Our results provide a genuine insight into how structural disordering and structural water improve sodium-ion storage in a layered electrode and open up an exciting direction for improving aqueous batteries.

25 ENERGY STORAGE↗
DOE OSTI2020

Extended experimental inferential structure determination method in determining the structural ensembles of disordered protein states

Proteins with intrinsic or unfolded state disorder comprise a new frontier in structural biology, requiring the characterization of diverse and dynamic structural ensembles. Here we introduce a comprehensive Bayesian framework, the Extended Experimental Inferential Structure Determination (X-EISD) method, which calculates the maximum log-likelihood of a disordered protein ensemble. X-EISD accounts for the uncertainties of a range of experimental data and back-calculation models from structures, including NMR chemical shifts, J-couplings, Nuclear Overhauser Effects (NOEs), paramagnetic relaxation enhancements (PREs), residual dipolar couplings (RDCs), hydrodynamic radii (R h ), single molecule fluorescence Förster resonance energy transfer (smFRET) and small angle X-ray scattering (SAXS). We apply X-EISD to the joint optimization against experimental data for the unfolded drkN SH3 domain and find that combining a local data type, such as chemical shifts or J-couplings, paired with long-ranged restraints such as NOEs, PREs or smFRET, yields structural ensembles in good agreement with all other data types if combined with representative IDP conformers.

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

High-pressure X-ray diffraction, Raman, and computational studies of MgCl 2 up to 1 Mbar: Extensive pressure stability of the β-MgCl 2 layered structure

We studied magnesium chloride (MgCl 2 ) with the rhombohedral layered CdCl 2 -type structure (α-MgCl 2 ), experimentally, using synchrotron angle-dispersive powder x-ray diffraction and Raman spectroscopy using a diamond-anvil cell up to 100 GPa at room temperature and theoretically using first-principles density functional calculations. Our results reveal a pressure-induced second-order structural phase transition to a hexagonal layered CdI 2 -type structure (β-MgCl 2 ) at 0.7 GPa: the stacking sequence of the Cl anions are altered resulting in a reduction of the c-axis length. Theoretical calculations confirm this phase transition sequence and the calculated transition pressure is in excellent agreement with the experiment. Lattice dynamics calculations also reproduce the experimental Raman spectra measured for the ambient and high-pressure phase. According to our experimental results MgCl 2 remains in a 2D layered phase up to 100 GPa and further, the 6-fold coordination of Mg cations is retained. Theoretical calculations of relative enthalpy suggest that this extensive pressure stability is due to a low enthalpy of the layered structure ruling out kinetic barrier effects. Our observation is unusual, as it contradicts with the general structural behavior of highly compressed AB 2 compounds.

36 MATERIALS SCIENCE↗
DOE OSTI2016

Simulations of cellulose translocation in the bacterial cellulose synthase suggest a regulatory mechanism for the dimeric structure of cellulose

The processive cycle of the bacterial cellulose synthase (Bcs) includes the addition of a single glucose moiety to the end of a growing cellulose chain followed by the translocation of the nascent chain across the plasma membrane. The mechanism of this translocation and its precise location within the processive cycle are not well understood. In particular, the molecular details of how a polymer (cellulose) whose basic structural unit is a dimer (cellobiose) can be constructed by adding one monomer (glucose) at a time are yet to be elucidated. Here, we have utilized molecular dynamics simulations and free energy calculations to the shed light on these questions. We find that translocation forward by one glucose unit is quite favorable energetically, giving a free energy stabilization of greater than 10 kcal mol-1. In addition, there is only a small barrier to translocation, implying that translocation is not rate limiting within the Bcs processive cycle (given experimental rates for cellulose synthesis in vitro). Perhaps most significantly, our results also indicate that steric constraints at the transmembrane tunnel entrance regulate the dimeric structure of cellulose. Namely, when a glucose molecule is added to the cellulose chain in the same orientation as the acceptor glucose, the terminal glucose freely rotates upon forward motion, thus suggesting a regulatory mechanism for the dimeric structure of cellulose. We characterize both the conserved and non-conserved enzyme-polysaccharide interactions that drive translocation, and find that 20 of the 25 residues that strongly interact with the translocating cellulose chain in the simulations are well conserved, mostly with polar or aromatic side chains. Our results also allow for a dynamical analysis of the role of the so-called 'finger helix' in cellulose translocation that has been observed structurally. Taken together, these findings aid in the elucidation of the translocation steps of the Bcs processive cycle and may be widely relevant to polysaccharide synthesizing or degrading enzymes that couple catalysis with chain translocation.

09 BIOMASS FUELS↗
DOE OSTI2017

Ensemble averaged structure–function relationship for nanocrystals: effective superparamagnetic Fe clusters with catalytically active Pt skin [Ensemble averaged structure-function relationship for composite nanocrystals: magnetic bcc Fe clusters with catalytically active fcc Pt skin]

Practical applications require the production and usage of metallic nanocrystals (NCs) in large ensembles. Besides, due to their cluster-bulk solid duality, metallic NCs exhibit a large degree of structural diversity. This poses the question as to what atomic-scale basis is to be used when the structure–function relationship for metallic NCs is to be quantified precisely. In this paper, we address the question by studying bi-functional Fe core-Pt skin type NCs optimized for practical applications. In particular, the cluster-like Fe core and skin-like Pt surface of the NCs exhibit superparamagnetic properties and a superb catalytic activity for the oxygen reduction reaction, respectively. We determine the atomic-scale structure of the NCs by non-traditional resonant high-energy X-ray diffraction coupled to atomic pair distribution function analysis. Using the experimental structure data we explain the observed magnetic and catalytic behavior of the NCs in a quantitative manner. Lastly, we demonstrate that NC ensemble-averaged 3D positions of atoms obtained by advanced X-ray scattering techniques are a very proper basis for not only establishing but also quantifying the structure–function relationship for the increasingly complex metallic NCs explored for practical applications.

36 MATERIALS SCIENCE↗