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At least 343 records · Page 19
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

RuBisCO activity assays: a simplified biochemical redox approach for in vitro quantification and an RNA sensor approach for in vivo monitoring

Abstract Background Ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) is the most abundant soluble protein in nature. Extensive studies have been conducted for improving its activity in photosynthesis through approaches like protein engineering. Concurrently, multiple biochemical and radiolabeling assays have been developed for determining its activity. Although these existing assays yield reliable results, they require addition of multiple external components, rendering them less convenient and expensive. Therefore, in this study, we have developed two relatively cheaper, convenient, and easily reproducible assays for quantitative and qualitative estimation of RuBisCO activity. Results We simplified a contemporary NADH based spectrophotometric RuBisCO assay by using cyanobacterial cell lysate as the source for Calvin cycle enzymes. We analyzed the influence of inorganic carbon substrates, CO 2 and NaHCO 3 , and varying protein concentrations on RuBisCO activity. Ribulose-1,5-bisphosphate (RuBP) consumption rates for the cultures grown under 5% CO 2 were 5–7 times higher than the ones grown with 20 mM NaHCO 3 , at different protein concentrations. The difference could be due to the impaired activity of carbonic anhydrase in the cell lysate, which is required for the conversion of HCO 3 − to CO 2 . The highest RuBisCO activity of 2.13 nmol of NAD + / µg of Chl-a/ min was observed with 50 µg of protein and 5% CO 2 . Additionally, we developed a novel RNA-sensor based fluorescence assay that is based on the principle of tracking the kinetics of ATP hydrolysis to ADP during the conversion of 3-phosphoglycerate (3-PG) to 1,3-bisphosphoglycerate (1,3-BPG) in the Calvin cycle. Under in vitro conditions, the fluorometric assay exhibited ~ 3.4-fold slower reaction rate (0.37 min −1 ) than the biochemical assay when using 5% CO 2 . We also confirmed the in vivo application of this assay, where increase in the fluorescence was observed with the recombinant strain of Synechocystis sp. PCC 6803 (SSL142) expressing the ADP-specific RNA sensor, compared to the WT. In addition, SSL142 exhibited three-fold higher fluorescence when supplemented with 20 mM NaHCO 3 as compared to the cells that were grown without NaHCO 3 supplementation. Conclusions Overall, we have developed a simplified biochemical assay for monitoring RuBisCO activity and demonstrated that it can provide reliable results as compared to the prior literature. Furthermore, the biochemical assay using 5% CO 2 (100% relative activity) provided faster RuBP consumption rate compared to the biochemical assay utilizing 20 mM NaHCO 3 (30.70% relative activity) and the in vitro fluorometric assay using 5% CO 2 (29.64% relative activity). Therefore, the absorbance-based biochemical assay using 5% CO 2 or higher would be suitable for in vitro quantification of the RuBisCO activity. On the other hand, the RNA-sensor based in vivo fluorometric assay can be applied for qualitative analysis and be used for high-throughput screening of RuBisCO variants. As RuBisCO is an enzyme shared amongst all the photoautotrophs, the assays developed in this study can easily be extended for analyzing the RuBisCO activities even in microalgae and higher plants.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1993

The seasonal evolution of reactive chlorine in the Northern Hemisphere stratosphere

In situ measurements of chlorine monoxide (ClO) at mid- and high northern latitudes are reported for the period October 1991 to February 1992. As early as mid-December and throughout the winter, significant enhancements of this ozone-destroying radical were observed within the polar vortex shortly after temperatures dropped below 195 K. Decreases in ClO observed in February were consistent with the rapid formation of chlorine nitrate (ClONO2) by recombination of ClO with nitrogen dioxide (NO2) released photochemically from nitric acid (HNO3). Outside the vortex, ClO abundances were higher than in previous years as a result of NO(x) suppression by heterogeneous reactions on sulfate aerosols enhanced by the eruption of Mount Pinatubo.

Toohey, D. W.↗
NASA NTRS2002

Crystallization and Preliminary X-ray Analysis of Der f 2, a Potent Allergen Derived from the House Dust Mite

Although a number of allergens have been identified and isolated, the underlying molecular basis for the potent immune response is poorly understood. House dust mites (Dermatophugoides sp.) are particularly ubiquitous contributors to atopy in developed countries. The rhinitis, dermatitis, and asthma associated with allergic reactions to these arthropods are often caused by relatively small (125-129 amino acids) mite proteins of unclear biological function. Der f 2, a major allergen from the mite Dermatophagoides farinae, has been recombinantly expressed and characterized. The Der f 2 protein has been crystallized in our laboratory and a native data set collected at a synchrotron source. The crystals belong to the orthorhombic space group I422 with unit cell parameters of a = 95.2 Angstroms, b = 95.2 Angstroms, and c = 103.3 Angstroms. An essentially complete (97.2%) data set has been collected to 2.4 Angstroms. Attempts to solve the crystal structure of Der f 2 by molecular replacement using the available NMR coordinates for either Der f 2 or Der p 2 (the homologous protein from D. pterovssinus) failed to reveal a creditable solution.

Roeber, Dana↗
NASA NTRS2003

Crystallization and preliminary X-ray analysis of Der f 2, a potent allergen derived from the house dust mite (Dermatophagoides farinae)

Although a number of allergens have been identified and isolated, the underlying molecular basis for the potent immune response is poorly understood. House dust mites (Dermatophagoides sp.) are ubiquitous contributors to atopy in developed countries. The rhinitis, dermatitis and asthma associated with allergic reactions to these arthropods are frequently caused by relatively small (125-129 amino acids) mite proteins of unknown biological function. Der f 2, a major allergen from the mite D. farinae, has been recombinantly expressed, characterized and crystallized. The crystals belong to the tetragonal space group I4(1)22, with unit-cell parameters a = b = 95.2, c = 103.3 A. An essentially complete (97.2%) data set has been collected to 2.4 A at a synchrotron source. Attempts to solve the crystal structure of Der f 2 by molecular replacement using the NMR coordinates for either Der f 2 or Der p 2 (the homologous protein from D. pteronyssinus) failed, but preliminary searches using the crystalline Der p 2 atomic coordinates appear to be promising.

Pyroglyphidae/chemistry/immunology↗
DOE OSTI2022

Electron-Stimulated Formation and Release of Molecular Hydrogen and Oxygen from Boehmite Nanoplatelet Films

Here, the production and release of H 2 and O 2 during and after electron (100–1000 eV) irradiation of boehmite nanoplatelet films was studied. H 2 and O 2 produced during irradiation likely correspond to electron-induced dissociation of the hydroxyls primarily in the terminal surface layers of the boehmite followed by the H· + H· → H 2 (g) and O + O → O 2 (g) combinative desorption reactions as well as the abstraction reactions H· + >OH – → H 2 (g) + >O·̅. Postirradiation temperature-programmed desorption shows a temperature-dependent release of H 2 but no additional release of O 2 . This process likely involves diffusion and recombination of H· atoms initially trapped between the γ-AlOOH planes followed by recombination at edge and surface sites. H 2 production upon thermal-annealing-irradiated material shows no dependence on incident electron flux, suggesting the precursor species (H·) trapped within the bulk are long-lived.

Jones, Brant M.↗
DOE OSTI2021

Cage effects control the mechanism of methane hydroxylation in zeolites

Catalytic conversion of methane to methanol remains an economically tantalizing but fundamentally challenging goal. Current technologies based on zeolites deactivate too rapidly for practical application. Here, we found that similar active sites hosted in different zeolite lattices can exhibit markedly different reactivity with methane, depending on the size of the zeolite pore apertures. Whereas zeolite with large pore apertures deactivates completely after a single turnover, 40% of active sites in zeolite with small pore apertures are regenerated, enabling a catalytic cycle. Detailed spectroscopic characterization of reaction intermediates and density functional theory calculations show that hindered diffusion through small pore apertures disfavors premature release of CH 3 radicals from the active site after C-H activation, thereby promoting radical recombination to form methanol rather than deactivated Fe-OCH 3 centers elsewhere in the lattice.

36 MATERIALS SCIENCE↗
NASA NTRS1992

Pathways of proton release in the bacteriorhodopsin photocycle

The pH dependencies of the rate constants in the photocycles of recombinant D96N and D115N/D96N bacteriorhodopsins were determined from time-resolved difference spectra between 70 ns and 420 ms after photoexcitation. The results were consistent with the model suggested earlier for proteins containing D96N substitution: BR hv----K----L----M1----M2----BR. Only the M2----M1 back-reaction was pH-dependent: its rate increased with increasing [H+] between pH 5 and 8. We conclude from quantitative analysis of this pH dependency that its reverse, the M1----M2 reaction, is linked to the release of a proton from a group with a pKa = 5.8. This suggests a model for wild-type bacteriorhodopsin in which at pH greater than 5.8 the transported proton is released on the extracellular side from this as yet unknown group and on the 100-microseconds time scale, but at pH less than 5.8, the proton release occurs from another residue and later in the photocycle most likely directly from D85 during the O----BR reaction. We postulate, on the other hand, that proton uptake on the cytoplasmic side will be by D96 and during the N----O reaction regardless of pH. The proton kinetics as measured with indicator dyes confirmed the unique prediction of this model: at pH greater than 6, proton release preceded proton uptake, but at pH less than 6, the release was delayed until after the uptake. The results indicated further that the overall M1----M2 reaction includes a second kinetic step in addition to proton release; this is probably the earlier postulated extracellular-to-cytoplasmic reorientation switch in the proton pump.

NASA Discipline Exobiology↗
DOE OSTI2023

Crystal structure of MbnF: an NADPH-dependent flavin monooxygenase from Methylocystis strain SB2

Methanobactins (MBs) are ribosomally produced and post-translationally modified peptides (RiPPs) that are used by methanotrophs for copper acquisition. The signature post-translational modification of MBs is the formation of two heterocyclic groups, either an oxazolone, pyrazinedione or imidazolone group, with an associated thioamide from an X -Cys dipeptide. The precursor peptide (MbnA) for MB formation is found in a gene cluster of MB-associated genes. The exact biosynthetic pathway of MB formation is not yet fully understood, and there are still uncharacterized proteins in some MB gene clusters, particularly those that produce pyrazinedione or imidazolone rings. One such protein is MbnF, which is proposed to be a flavin monooxygenase (FMO) based on homology. To help to elucidate its possible function, MbnF from Methylocystis sp. strain SB2 was recombinantly produced in Escherichia coli and its X-ray crystal structure was resolved to 2.6 Å resolution. Based on its structural features, MbnF appears to be a type A FMO, most of which catalyze hydroxylation reactions. Preliminary functional characterization shows that MbnF preferentially oxidizes NADPH over NADH, supporting NAD(P)H-mediated flavin reduction, which is the initial step in the reaction cycle of several type A FMO enzymes. It is also shown that MbnF binds the precursor peptide for MB, with subsequent loss of the leader peptide sequence as well as the last three C-terminal amino acids, suggesting that MbnF might be needed for this process to occur. Finally, molecular-dynamics simulations revealed a channel in MbnF that is capable of accommodating the core MbnA fragment minus the three C-terminal amino acids.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1985

Space shuttle ram glow: Implication of NO2 recombination continuum

The ram glow data gathered to data from imaging experiments on space shuttle suggest the glow is a continuum (within 34 angstrom resolution); the continuum shape is such that the peak is near 7000 angstroms decreasing to the blue and red, and the average molecular travel leading to emission after leaving the surface is 20 cm (assuming isotropic scattering from the surface). Emission continuum is rare in molecular systems but the measured spectrum does resemble the laboratory spectrum of NO2 (B) recombination continuum. The thickness of the observed emission is consistent with the NO2 hypothesis given an exit velocity of approx. 2.5 km/sec (1.3 eV) which leaves approx. 3.7 eV of ramming OI energy available for unbonding the recombined NO2 from the surface. The NO2 is formed in a 3-body recombination of OI + NO + m = NO2 + m where OI originates from the atmosphere and NO is chemically formed on the surface from atmospheric NI and OI. The spacecraft surface then acts as the n for the reaction: Evidence exists from orbital mass spectrometer data that the NO and NO2 chemistry described in this process does occur on surfaces of spectrometer orifices in orbit. Surface temperature effects are likely a factor in the NO sticking efficiency and, therefore, glow intensities.

Swenson, G. R.↗
DOE OSTI2021

Design Principles for Efficient and Stable Water Splitting Photoelectrocatalysts

Photoelectrochemical water splitting is a promising avenue for sustainable production of hydrogen used in the chemical industry and hydrogen fuel cells. The basic components of most photoelectrochemical water splitting systems are semiconductor light absorbers coupled to electrocatalysts, which perform the desired chemical reactions. A critical challenge for the design of these systems is the lack of stability for the majority of desired semiconductors under operating water splitting conditions. One strategy to address this issue is to protect the semiconductor by covering it with a stabilizing insulator layer, creating a metal–insulator–semiconductor (MIS) architecture, which has demonstrated improved stability. In addition to enhanced stability, the insulator layer may significantly affect the electron and hole transfer, which governs the recombination rates. Furthermore, the insertion of an insulator layer leads to the introduction of additional insulator/electrocatalyst and insulator/semiconductor interfaces. These interfaces can impact the system’s performance significantly, and they need to be carefully engineered to optimize the efficiencies of MIS systems. In this Account, we describe our recent progress in shedding light on the critical role of the insulator and the interfaces on the performance of MIS systems. We discuss our findings by focusing on the concrete example of planar n-type Si protected by a HfO 2 insulator layer and coupled to a Ni or Ir electrocatalyst that performs the oxygen evolution reaction, one of the water splitting half-reactions. To improve our fundamental understanding of the insulator layer, we precisely control the HfO 2 insulator thickness using atomic layer deposition (ALD), and we perform a series of rigorous electrochemical experiments coupled with theory and modeling. We demonstrate that by tuning the insulator thickness, we can control the flux and recombination of photogenerated electrons and holes to optimize the generated photovoltage. Despite optimizing the thickness, we find that the maximum generated photovoltage in MIS systems is often significantly lower than the upper performance limit, i.e., there are additional losses in the system that could not be addressed by optimizing the insulator thickness. We identify the sources of these losses and describe strategies to minimize them by a combination of improving the semiconductor light absorption, removing nonidealities associated with interfacial defects, and finding alternative insulators with improved charge carrier selectivity. Finally, we quantify the improvements that can be obtained by implementing these specific strategies. Our collective work outlines strategies to analyze MIS systems, identify the sources of efficiency losses, and optimize the design to approach the fundamental performance limits. Furthermore, these general approaches are broadly applicable to photoelectrochemical materials that utilize sunlight to produce value-added chemicals.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1979

Refinement of the aeronomically determined rate coefficient for the reaction of N2/+/ with O

An earlier aeronomic determination of the rate coefficient for the reaction N2(+) + O yields NO(+) + N using Atmosphere Explorer data indicated a small increase in the rate coefficient with ion temperature, contrary to laboratory observations. This was incorrectly attributed to neglect of an increase in the N2(+) recombination rate with vibrational excitation. Recent aeronomical results have shown that the rate coefficient for charge exchange of O(+)(2D) with N2 is about an order of magnitude smaller at thermal temperatures than at energies greater than 0.5 eV (i.e., energies at which laboratory measurements have been made). It is shown that the use of the smaller charge exchange rate coefficient coupled with recent results on N2 quenching of O(+)(2D) yields a temperature dependence in excellent agreement with the laboratory results for the rate coefficient.

Torr, D. G.↗
NASA NTRS1989

The 630 nm dayglow

The daytime thermospheric emission at 630 nm from the (3P-1D) transition of atomic oxygen is examined using data from the Atmosphere Explorer C and E spacecraft. Observed altitude distributions of the emission rate measured using the Visible Airglow Experiment are compared with those calculated from in situ measurements of ion and neutral densities and temperatures, and from a model of the photon and photoelectron flux. Good agreement is obtained for most orbits with photoelectron impact on O, photodissociation of O2, and dissociative recombination of O2(+) providing most of the production. Implications for some of the controversial points of O(1D) chemistry, such as the solar EUV and Schumann-Runge continuum flux, the yield of O(1D) from the reaction of N(2D) with O2, the value of spontaneous transition coefficients, and the rate of quenching by O(3P) are discussed.

Solomon, Stanley C.↗
DOE OSTI2022

Harnessing Intermolecular Interactions to Promote Long-Lived Photoinduced Charge Separation from Copper Phenanthroline Chromophores

In this study, facilitating photoinduced electron transfer (PET) while minimizing rapid charge-recombination processes to produce a long-lived charge-separated (CS) state represents a primary challenge associated with achieving efficient solar fuel production. Natural photosynthetic systems employ intermolecular interactions to arrange the electron-transfer relay in reaction centers and promote a directional flow of electrons. This work explores a similar tactic through the synthesis and ground- and excited-state characterization of two Cu(I)bis(phenanthroline) chromophores with homoleptic and heteroleptic coordination geometries and which are functionalized with negatively charged sulfonate groups. The addition of sulfonate groups enables solubility in pure water, and it also induces assembly with the dicationic electron acceptor methyl viologen (MV 2+ ) via bimolecular, dynamic electrostatic interactions. The effect of the sulfonate groups on the ground- and excited-state properties was evaluated by comparison with the unsulfonated analogues in 1:1 acetonitrile/water. The excited-state lifetimes for all sulfonated complexes are similar to what we expect from previous literature, with the exception of the sulfonated heteroleptic complex whose metal-to-ligand charge-transfer (MLCT) lifetime in water has two components that are fit to 10 and 77 ns. For the sulfonated complexes, we detected reduced MV +$\bullet$ in both solvent environments following MLCT excitation, but control measurements in 1:1 acetonitrile/water with the unsulfonated analogues showed no PET to MV 2+ , indicating that electrostatically driven supramolecular assemblies of the sulfonated complexes with MV 2+ facilitate the observed PET. Additionally, the strength of the intermolecular interactions driving the formation of these assemblies changes drastically with the solvent environment. In 1:1 acetonitrile/water, PET occurred from both sulfonated complexes with quantum yields (Φ ET ) of 2-3% but increased to a remarkable 98% for the sulfonated heteroleptic complex with a 3 μs CS-state lifetime in water.

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

Catalytic reforming of methane with H 2 S via dynamically stabilized sulfur on transition metal oxides and sulfides

Reforming of methane with H 2 S is a promising path to directly utilize sour natural gas reserves, although some aspects of the mechanism and structure–function relations remain elusive. In this report we show that metal oxides of group 4–6 elements, which are inert for steam and dry methane reforming reactions, are active and stable (pre)catalysts for the H 2 S reforming of methane. The key active sites are sulfur species (S*) that are dynamically bound to metal cations during catalysis. Similar H/D isotope exchange patterns and universal rate inhibition by H 2 on representative catalysts indicate that H 2 S decomposition and recombination of surface hydrogen atoms are quasi-equilibrated, whereas CH 4 dissociation steps are reversible, yet not quasi-equilibrated. An in-depth analysis of the kinetic data and isotopic substitution effects identifies S*-mediated C–H bond cleavage as the most plausible rate-limiting step common for all catalysts, with subtle yet essential differences between 3d and 4d/5d catalysts in the thermodynamic stability of S*.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Nature of molybdenum carbide surfaces for catalytic hydrogen dissociation using machine-learned potentials: an ensemble-averaged perspective

Molybdenum carbides with an electronic structure similar to noble metals have gained attention as a promising low-cost catalyst for biomass valorization and the hydrogen evolution reaction. However, our fundamental understanding of the catalyst surface and how different phases of these catalysts behave at varying reaction conditions is limited to ground state density functional theory calculations as ab initio molecular dynamics (AIMD) is computationally prohibitive at relevant length and time scales. Here, in this work, we train a multi-atomic cluster expansion (MACE) machine-learned interatomic potentials (MLIP) to study hydrogen dissociation and dynamics over Mo, δ-MoC, α-Mo 2 C, and β-Mo 2 C surfaces at varying temperatures and hydrogen partial pressures. Our simulations identify unique and different molecular and atomic hydrogen adsorption sites on different surfaces that do not depend on the temperature. At low hydrogen pressures, the surface coverage is monolayer, which transitions to two-layer adsorption at higher pressures. We find that atomic hydrogen diffusion and recombinations are preferred over molybdenum atom hollow sites, while the diffusion over carbon-terminated facets was negligible, signifying particularly strong C–H interactions. In contrast, molecular hydrogen adsorption occurs mostly atop Mo or the bridging sites. At a comparable hydrogen loading, β-Mo 2 C (001) is the most active surface for hydrogen dissociation reaction. This work provides insights into the dynamic nature of the hydrogen dissociation chemistry and the diversity of hydrogen adsorption sites on molybdenum carbides.

08 HYDROGEN↗
DOE OSTI2023

BiVO 4 –Liquid Junction Photovoltaic Cell with 0.2% Solar Energy Conversion Efficiency

BiVO 4 is an important photoanode material for water oxidation, but its photoelectrochemistry regarding the triiodide/iodide redox couple is not well understood. Here, we use a combination of open circuit potential measurements, photoelectrochemical scans, and liquid surface photovoltage spectroscopy (SPS) to confirm that BiVO 4 /triiodide/iodide electrolyte contacts produce up to 0.55 V photovoltage under 23 mW/cm –2 illumination from a 470 nm LED. Inspired by these results, we construct FTO/BiVO 4 /KI(I 2 ) aq /Pt sandwich photoelectrochemical cells from electrochemically grown 0.5 × 0.5 cm 2 BiVO 4 and Mo-doped BiVO 4 films. Under AM 1.5 illumination, the devices have up to 0.22% energy conversion efficiency, 0.32 V photovoltage, and 1.8 mA cm –2 photocurrent. Based on SPS, hole transfer to iodide is sufficiently fast to prevent the competing water oxidation reaction. Mo doping increases the incident photon-to-current efficiency to up to 55% (at 425 nm under front illumination) by improving the BiVO 4 conductivity, but this comes at the expense of a lower photovoltage resulting from recombination at the Mo defects and a detrimental Schottky junction at the interface with FTO. Additional photovoltage losses are caused by the offset between the BiVO 4 valence band edge and the triiodide/iodide electrochemical potential and by electron back transfer to iodide at the FTO back contact (shunting). Overall, this work provides the first example of a BiVO 4 –liquid photovoltaic cell and an analysis of its limitations. Finally, even though the larger band gaps of metal oxides constrain their solar energy conversion efficiency, their transparency to visible light and deep valence bands makes them suitable for tandem photovoltaic devices.

14 SOLAR ENERGY↗
DOE OSTI2023

Anti-Arrhenius behavior of electron transfer reactions in molecular dimers

Rates of chemical reactions typically accelerate as the temperature rises, following the Arrhenius law. However, electron transfer reactions may exhibit weak temperature dependence or counterintuitive behavior, known as anti-Arrhenius behavior, wherein reaction rates decrease as temperature increases. Solvent reorganization energy and torsion-induced changes in electronic couplings could contribute to this unusual behavior, but how each contributes to the overall temperature dependence is unclear. One can decelerate the charge recombination process in photogenerated radical pairs or charge-separated states by harnessing this often-overlooked phenomenon. This means that we could achieve long-lived radical pairs without relying on conventional cooling. Using a series of homo molecular dimers, we showed that the degree of torsional hindrance dictates temperature-dependent torsion-induced changes in electronic coupling and, therefore, charge recombination rates. The overall temperature dependence is controlled by how changes in electronic coupling and the temperature-dependent solvent reorganization energy contribute to the rates of charge recombination. Our findings pave the way for rationally designing molecules that exhibit anti-Arrhenius behavior to slow down charge recombination, opening possibilities for applications in energy-related and quantum information technologies.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗