Search NASA⌕ Search

SEARCH · Search NASA

Results for “Binding distance”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

169 records · Page 10
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Structural and Catalytic Properties of Isolated Pt 2+ Sites in Platinum Phosphide (PtP 2 )

This article describes the synthesis and catalytic properties of supported, 2-3 nm platinum phosphide (PtP 2 ) nanoparticles (NPs). Depending on the P loading, two PtP 2 structures are formed, that is, a PtP 2 surface on a (metallic) Pt core (Pt@PtP 2 ) and single-phase PtP 2 NPs. The structures were determined using extended X-ray absorption fine structure , in situ synchrotron X-ray diffraction, and scanning transmission electron microscopy. In PtP 2 NPs, Pt 2+ ions are geometrically isolated by P 2 2- ions, at a Pt-Pt distance of 4.02 Å, which is much longer than 2.78 Å in (metallic) Pt NPs. The oxidation state of Pt in PtP 2 NPs was determined by in situ X-ray absorption near-edge structure and in situ X-ray photoelectron spectroscopy and was found to be consistent with Pt 2+ ions even after treatment in H 2 at 550 °C. Unlike Pt NPs, which are highly active for propylene hydrogenation at room temperature, PtP 2 NPs are not active below about 150 °C, suggesting the absence of metallic surface Pt. In contrast to metallic Pt, which is poorly selective for acetylene hydrogenation, PtP 2 NPs display high selectivity toward ethylene. PtP 2 , also has high olefin selectivity for propane dehydrogenation, although the rate per g Pt is about 7 times lower than that of metallic Pt NPs of the same size. In situ resonant inelastic X-ray scattering spectroscopy shows that the energy of the filled Pt 5d valence orbitals is 1.5 eV lower than that of metallic Pt, which leads to weaker adsorbate binding consistent with its catalytic properties. Here, a H 2 -stable Pt 2+ site suggests different catalytic applications for these catalysts as compared to Pt NPs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS2003

Structural Basis for Flip-Flop Action of Thiamin Pyrophosphate-Dependent Enzymes Revealed by Human Pyruvate Dehydrogenase

Thiamin pyrophosphate (TPP), the biologically active form of vitamin BI, is a cofactor of enzymes catalyzing reactions involving the cleavage of a carbon-carbon bond adjacent to an oxo group. TPP-dependent enzymes show a common mechanism of TPP activation by: (1) forming the ionic N-H...O(sup -) hydrogen bonding between the N1' atom of the aminopirymidine ring of the coenzyme and intrinsic gamma-carboxylate group of glutamate and (2) imposing an "active" V-conformation that brings the N4' atom of the aminopirymidine to the distance required for the intramolecular C-H.. .N hydrogen bonding with the thiazolium C2 atom. Within these two hydrogen bonds that rapidly exchange protons, protonation of the N1' atom is strictly coordinated with the deprotonation of the 4' -amino group and eventually abstraction of the proton from C2. The human pyruvate dehydrogenase Elp, component of human pyruvate dehydrogenase complex, catalyzes the irreversible decarboxylation of the pyruvate followed by the reductive acetylation of the lipoyl group of dihydrolipoyl acyltransferase. Elp is alpha(sub 2)beta(sub2)-heterotetrameric with a molecular mass of I54 kDa, which has two catalytic sites, each providing TPP and magnesium ion as cofactors and each formed on the interface between the PP and PYR domains. The dynamic nonequivalence of two otherwise chemically equivalent catalytic sites has been observed and the flip-flop mechanism was suggested, according to which two active sites affect each other and in which different steps of the catalytic reaction are performed in each of the sites at any given moment. Based on specific futures of human pyruvate dehydrogenase including rigid and flexible connections between domains that bind the cofactor we propose a mechanistic model for the flip-flop action of this enzyme. We postulate that the dynamic protein environment drives the exchange of tautomers in the 4' -aminopyrimidine ring of the cofactor through a concerted shuttl-like motion of tightly connected domains. The dynamic exchange of those tautomers, in turns, is required during the reactions of pyruvate decarboxylation and reductive acetylation of lipoamide. Thus the shuttle-like motion of the domains is coordinated with the reactions of decarboxylation and acetylation, which are carried out in each of the cofactor sites resulting in a flip-flop action of the enzyme. The structure-derived mechanism of action of human pyruvate dehydrogenase may be likely common for other TPP-dependent enzymes.

Dominiak, Paulina↗
DOE OSTI2025

Investigation of the Effect of Framework Flexibility on CO 2 Adsorption in SIFSIX-3-Cu Using a Machine-Learned Force Field

Metal–organic frameworks (MOFs) offer promise as selective CO 2 sorbents, but successful MOF sorbent materials need high CO 2 binding affinity and selectivity for CO 2 over water. This work focuses on the use of machine-learned force fields (MLFFs) to model CO 2 adsorption in flexible MOFs, with a focus on SIFSIX-3-Cu, an anion-pillared MOF known for its high CO 2 affinity. A preliminary high-throughput screening of over 900 anion-pillared MOFs was performed using rigid UFF+DDEC6 force fields to predict zero-loading heats of adsorption for CO 2 and H 2 O. SIFSIX-3-Cu was selected for further computational study due to its predicted CO 2 heat of adsorption and experimental relevance. A DeePMD-based MLFF was trained to reproduce DFT (PBE+D3) energies and forces, with an iterative sampling scheme combining molecular dynamics, geometry optimization, random geometric insertion, and NVT Monte Carlo-based configuration generation to capture both attractive and repulsive regions of the potential energy surface. Flexibility of the MOF was explicitly included, contrasting with previous models that approximated the MOF as rigid. Hybrid Monte Carlo/molecular dynamics (MC/MD) simulations with the MLFF produced CO 2 adsorption isotherms in good agreement with experimental data at direct air capture (DAC) pressures (e.g., 40 Pa), in contrast to previous overestimations of CO 2 sorption by models with rigid structures. Bond and angle histogram analysis showed that MOF flexibility increased the variance of fluorine–fluorine diagonal distances at adsorption sites, resulting in a lower predicted sorption for flexible, asymmetric SIFSIX-3-Cu pore geometries compared to the rigid, symmetric DFT-optimized SIFSIX-3-Cu pore geometry. A detailed description of flexibility afforded by the MLFF resulted in an accurately predicted CO 2 uptake (0.88 mmol/g) at low pressure (40 Pa) compared to the experimentally measured value (1.24 mmol/g). In conclusion, these results underscore the importance of including framework flexibility when modeling adsorption phenomena in MOFs, particularly for low-pressure applications.

adsorption↗
NASA NTRS2017

Computational Modeling to Limit the Impact Displays and Indicator Lights Have on Habitable Volume Operational Lighting Constraints

NASA has demonstrated an interest in improving astronaut health and performance through the installment of a new lighting countermeasure on the International Space Station. The Solid State Lighting Assembly (SSLA) system is designed to positively influence astronaut health by providing a daily change to light spectrum to improve circadian entrainment. Unfortunately, existing NASA standards and requirements define ambient light level requirements for crew sleep and other tasks, yet the number of light-emitting diode (LED) indicators and displays within a habitable volume is currently uncontrolled. Because each of these light sources has its own unique spectral properties, the additive lighting environment ends up becoming something different from what was planned or researched. Restricting the use of displays and indicators is not a solution because these systems provide beneficial feedback to the crew. The research team for this grant used computer-based computational modeling and real-world lighting mockups to document the impact that light sources other than the ambient lighting system contribute to the ambient spectral lighting environment. In particular, the team was focused on understanding the impacts of long-term tasks located in front of avionics or computer displays. The team also wanted to understand options for mitigating the changes to the ambient light spectrum in the interest of maintaining the performance of a lighting countermeasure. The project utilized a variety of physical and computer-based simulations to determine direct relationships between system implementation and light spectrum. Using real-world data, computer models were built in the commercially available optics analysis software Zemax Optics Studio(c). The team also built a mockup test facility that had the same volume and configuration as one of the Zemax models. The team collected over 1200 spectral irradiance measurements, each representing a different configuration of the mockup. Analysis of the data showed a measurable impact on ambient light spectrum. This data showed that obvious design techniques exist that can be used to bind the ambient light spectrum closer to the planned spectral operating environment for the observer's eye point. The following observations should be considered when designing an operational environment that is dominated by computer displays. When more light is directed into the field of view of the observer, the greater the impact it will make on various human factors issues that depend on spectral shape and intensity. Because viewing angle has a large part to play in the amount of light flux on the crewmember's retina, beam shape, combined with light source location is an important factor for determining percent probable incident flux on the observer from any combination of light sources. Computer graphics design and display lumen output are major factors influencing the amount of spectrally intense light projected into the environment and in the viewer's direction. Use of adjustable white point display software was useful only if the predominant background color was white and if it matched the ambient light system's color. Display graphics that used a predominantly black background had the least influence on unplanned spectral energy projected into the environment. Percent reflectance makes a difference in total energy reflected back into an environment, and within certain architectural geometries, reflectance can be used to control the amount of a light spectrum that is allowed to perpetuate in the environment. Data showed that room volume and distance from significant light sources influence the total spectrum in a room. Smaller environments had a homogenizing effect on total light spectrum, whereas light from multiple sources in larger environments was less mixed. The findings indicated above should be considered when making recommendations for practice or standards for architectural systems. The ambient lighting system, surface reflectance, and display and indicator implementation all factor into the users' spectral environment. A variety of low-cost solutions exist to mitigate the impact of light from non-architectural lighting systems, and much potential for system automation and integration of display systems with the ambient environment. This team believes that proper planning can be used to avoid integration problems and also believes that human-in-the-loop evaluations, real-world test and measurement, and computer modeling can be used to determine how changes to a process, display graphics, and architecture will help maintain the planned spectral operating lighting environment.

Clark, T. A.↗
NASA NTRS1995

ROSAT PSPC observations of the early-type galaxies NGC 507 and NGC 499: Central cooling and mass determination

We present the results of a deep observation of NGC 507 and NGC 499 with the ROSAT Position Sensitive Proportional Counter (PSPC). The X-ray emission of NGC 507 is extended at least out to 1000 sec (458 kpc at a distance of 94.5 Mpc). The radial profile of X-ray surface brightness goes as Sigma(sub x) is approximately r(exp -1.8) outside the core region. The radial profile is a function of energy such that the softer X-rays have a smaller core radius and a flatter slope. Spectral analysis reveals that the emission temperature, with an average of 1 keV, peaks at an intermediate radius of 2-3 min and falls toward the center (possibly decreases outward as well). The absorption column density is consistent with the Galactic line-of-sight value. The X-ray emission of NGC 499 is extended to 300 sec and suggests a similarly cooler core. The cooler cores of NGC 507 and NGC 499 are strong evidence of the presence of cooling flows in these galaxies. Assuming hydrostatic equilibrium outside the cooling radius, the estimated mass-to-light ratio of NGC 507 is 97 +/- 16 within 458 kpc, indicative of the presence of a heavy halo. Similarly, the mass-to-light ratio of NGC 499 is 89 +/- 14 within 137 kpc. Near the edge of the X-ray-emitting region of NGC 507 we detect 19 soft, unresolved sources. These sources do not have optical counterparts and are significantly in excess of the expected number of background serendipitous sources. We speculate that they may represent cooling clumps in the halo of NGC 507. If there are many undetected cooling clumps distributed at large radii, then the radial profile of the X-ray surface brightness does not directly reflect the potential, adding uncertainty to the measurement of the binding mass; the gas mass could also be overestimated.

Kim, Dong-Woo↗
DOE OSTI2022

Loss of Multiple ABCB Auxin Transporters Recapitulates the Major twisted dwarf 1 Phenotypes in Arabidopsis thaliana

FK506-BINDING PROTEIN 42/TWISTED DWARF 1 (FKBP42/TWD1) directly regulates cellular trafficking and activation of multiple ATP-BINDING CASSETTE (ABC) transporters from the ABCB and ABCC subfamilies. abcb1 abcb19 double mutants exhibit remarkable phenotypic overlap with twd1 including severe dwarfism, stamen elongation defects, and compact circinate leaves; however, twd1 mutants exhibit greater loss of polar auxin transport and additional helical twisting of roots, inflorescences, and siliques. As abcc1 abcc2 mutants do not exhibit any visible phenotypes and TWD1 does not interact with PIN or AUX1/LAX auxin transporters, loss of function of other ABCB auxin transporters is hypothesized to underly the remaining morphological phenotypes. Here, gene expression, mutant analyses, pharmacological inhibitor studies, auxin transport assays, and direct auxin quantitations were used to determine the relative contributions of loss of other reported ABCB auxin transporters (4, 6, 11, 14, 20, and 21) to twd1 phenotypes. From these analyses, the additional reduction in plant height and the twisted inflorescence, root, and silique phenotypes observed in twd1 compared to abcb1 abcb19 result from loss of ABCB6 and ABCB20 function. Additionally, abcb6 abcb20 root twisting exhibited the same sensitivity to the auxin transport inhibitor 1-napthalthalamic acid as twd1 suggesting they are the primary contributors to these auxin-dependent organ twisting phenotypes. The lack of obvious phenotypes in higher order abcb4 and abcb21 mutants suggests that the functional loss of these transporters does not contribute to twd1 root or shoot twisting. Analyses of ABCB11 and ABCB14 function revealed capacity for auxin transport; however, their activities are readily outcompeted by other substrates, suggesting alternate functions in planta, consistent with a spectrum of relative substrate affinities among ABCB transporters. Overall, the results presented here suggest that the ABCB1/19 and ABCB6/20 pairs represent the primary long-distance ABCB auxin transporters in Arabidopsis and account for all reported twd1 morphological phenotypes. Other ABCB transporters appear to participate in highly localized auxin streams or mobilize alternate transport substrates.

54 ENVIRONMENTAL SCIENCES↗
NASA NTRS2002

Tetragonal Lysozyme Nucleation and Crystal Growth: The Role of the Solution Phase

Lysozyme, and most particularly the tetragonal form of the protein, has become the default standard protein for use in macromolecule crystal nucleation and growth studies. There is a substantial body of experimental evidence, from this and other laboratories, that strongly suggests this proteins crystal nucleation and growth is by addition of associated species that are preformed by standard reversible concentration-driven self association processes in the bulk solution. The evidence includes high resolution AFM studies of the surface packing and of growth unit size at incorporation, fluorescence resonance energy transfer measurements of intermolecular distances in dilute solution, dialysis kinetics, and modeling of the growth rate data. We have developed a selfassociation model for the proteins crystal nucleation and growth. The model accounts for the obtained crystal symmetry, explains the observed surface structures, and shows the importance of the symmetry obtained by self-association in solution to the process as a whole. Further, it indicates that nucleation and crystal growth are not distinct mechanistically, but identical, with the primary difference being the probability that the particle will continue to grow or dissolve. This model also offers a possible mechanism for fluid flow effects on the growth process and how microgravity may affect it. While a single lysozyme molecule is relatively small (M.W. = 14,400), a structured octamer in the 4(sub 3) helix configuration (the proposed average sized growth unit) would have a M.W. = 115,000 and dimensions of 5.6 x 5.6 x 7.6 nm. Direct AFM measurements of growth unit incorporation indicate that units as wide as 11.2 nm and as long as 11.4 nm commonly attach to the crystal. These measurements were made at approximately saturation conditions, and they reflect the sizes of species that both added or desorbed from the crystal surface. The larger and less isotropic the associated species the more likely that it will be oriented to some degree in a flowing boundary layer, even at the low flow velocities measured about macromolecule crystals. Flow-driven effects resulting in misorientation upon addition to and incorporation into the crystal need only be a small fraction of a percentage to significantly affect the resulting crystal. One Earth, concentration gradient driven flow will maintain a high interfacial concentration, i.e., a high level (essentially that of the bulk solution) of solute association at the interface and higher growth rate. Higher growth rates mean an increased probability that misaligned growth units are trapped by subsequent growth layers before they can be desorbed and try again, or that the desorbing species will be smaller than the adsorbing species. In microgravity the extended diffusive boundary layer will lower the interfacial concentration. This results in a net dissociation of aggregated species that diffuse in from the bulk solution, i.e., smaller associated species, which are more likely able to make multiple attempts to correctly bind, yielding higher quality crystals.

Pusey, Marc L.↗