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At least 55 records · Page 3

Catalysis of hydrolysis and nucleophilic substitution at the P-N bond of phosphoimidazolide-activated nucleotides in phosphate buffers

Phosphoimidazolide-activated derivatives of guanosine and cytidine 5'-monophosphates, henceforth called ImpN's, exhibit enhanced rates of degradation in the presence of aqueous inorganic phosphate in the range 4.0 < or = pH < or = 8.6. This degradation is been attributed to (i) nucleophilic substitution of the imidazolide and (ii) catalysis of the P-N bond hydrolysis by phosphate. The first reaction results in the formation of nucleoside 5'-diphosphate and the second in nucleoside 5'-monophosphate. Analysis of the observed rates as well as the product ratios as a function of pH and phosphate concentration allow distinction between various mechanistic possibilities. The results show that both H2PO4- and HPO4(2-) participate in both hydrolysis and nucleophilic substitution. Statistically corrected biomolecular rate constants indicate that the dianion is 4 times more effective as a general base than the monoanion, and 8 times more effective as nucleophile. The low Bronsted value beta = 0.15 calculated for these phosphate species, presumed to act as general bases in facilitating water attack, is consistent with the fact that catalysis of the hydrolysis of the P-N bond in ImpN's has not been detected before. The beta nuc = 0.35 calculated for water, H2PO4-, HPO4(2-), and hydroxide acting as nucleophiles indicates a more associative transition state for nucleotidyl (O2POR- with R = nucleoside) transfers than that observed for phosphoryl (PO3(2-)) transfers (beta nuc = 0.25). With respect to the stability/reactivity of ImpN's under prebiotic conditions, our study shows that these materials would not suffer additional degradation due to inorganic phosphate, assuming the concentrations of phosphate, Pi, on prebiotic Earth were similar to those in the present oceans ([Pi] approximately 2.25 micromoles).

NASA Discipline Number 52-20↗

Geological Factors Impacted Cadmium Availability and use as an Alternative Cofactor for Zinc in the Carbon Fixation Pathways of Marine Diatoms

Transition metal cofactors are crucial for many biological processes. Despite being primarily considered to be toxic, the transition metal cadmium (Cd) was discovered to be a substitute cofactor for zinc (Zn) in photosynthetic carbon fixation pathways of marine diatoms. However, it is not known how conditions in the geosphere impacted Cd availability and its incorporation as an alternative metal cofactor for phytoplankton. We employed mineral chemistry network analysis to investigate which geochemical factors may have influenced the availability of Cd and Zn during the putative time period that the alternative Cd-based pathway evolved. Our results show that Zn minerals are more chemically diverse than are Cd minerals, but Zn- and Cd-containing minerals have similar network centrality values when specifically considering sulfur (S)-containing species. Cadmium and Zn sulfides are the most common Cd- and Zn-containing mineral species over the past 500 million years. In particular, the Cd and Zn sulfides, respectively greenockite and sphalerite, were highly abundant during this time period. Furthermore, S-containing Cd and Zn minerals are commonly co-located in geologic time, allowing them to be weathered and transported to the ocean in tandem, rather than from separate sources. We suggest that the simultaneous weathering of Cd and Zn sulfides allowed for Cd to be a bioavailable direct substitute for Zn in protein complexes during periods of Zn depletion. The biogeochemical cycles of Zn and Cd exemplify the importance of the coevolution of the geosphere and biosphere in shaping primary production in the modern ocean.

Naman Srivastava↗

Liquid rocket combustor computer code development

The Advanced Rocket Injector/Combustor Code (ARICC) that has been developed to model the complete chemical/fluid/thermal processes occurring inside rocket combustion chambers are highlighted. The code, derived from the CONCHAS-SPRAY code originally developed at Los Alamos National Laboratory incorporates powerful features such as the ability to model complex injector combustion chamber geometries, Lagrangian tracking of droplets, full chemical equilibrium and kinetic reactions for multiple species, a fractional volume of fluid (VOF) description of liquid jet injection in addition to the gaseous phase fluid dynamics, and turbulent mass, energy, and momentum transport. Atomization and droplet dynamic models from earlier generation codes are transplated into the present code. Currently, ARICC is specialized for liquid oxygen/hydrogen propellants, although other fuel/oxidizer pairs can be easily substituted.

Liang, P. Y.↗

Detections of C-13-substituted C3H2 in astronomical sources

The more abundant C-13-substituted variant of the new interstellar ring molecule, C3H2, has been detected in TMC-1 and Sgr B2, and a tentative detection has been made in IRC + 10216. The fractional abundance relative to H2 is 1-2 x 10 to the -8th in TMC-1, a value similar to that of HCN. In Sgr B2, the C-12 species shows a self-absorbed profile and the relative abundance of C3H2 is about an order of magnitude less than in TMC-1. In IRC + 10216, the fractional abundance of C3H2 is an order of magnitude greater than that in TMC-1.

Madden, Suzanne C.↗

Development of the gametophyte of the fern Schizaea pusilla

Schizaea pusilla is a pteridophyte with several unique developmental characteristics. In contrast to most other fern species, S. pusilla gametophytes remain filamentous throughout their development, and the gametophytes are associated with an endophytic fungus which appears to be mycorrhizal. In terms of tropistic responses, apical filament cells of young gametophytes are negatively phototropic compared with germ filaments of other ferns which exhibit positive phototropism. Cryofixation (propane jet freezing and high-pressure freezing) in conjunction with freeze substitution electron microscopy was used to study young gametophytes. The results demonstrate that apical filament cells have a distinctive structural polarity and that rhizoids also can be successfully frozen by these methods. The cytoskeleton and endomembrane system were particularly well preserved in cryofixed cells. In addition, Schizaea gametophytes were used as a test system to evaluate potential artifacts of propane jet freezing and high pressure freezing. There was little apparent difference in ultrastructure between cells cryofixed by either freezing method. These gametophytes will be useful in determining the effectiveness of cryofixation techniques and as a model system in tip growth studies.

Non-NASA Center↗

Dissociative recombination of O2(+), NO(+) and N2(+)

A new L(2) approach for the calculation of the threshold molecular capture width needed for the determination of DR cross sections was developed. The widths are calculated with Fermi's golden rule by substituting Rydberg orbitals for the free electron continuum coulomb orbital. It is shown that the calculated width converges exponentially as the effective principal quantum number of the Rydberg orbital increases. The threshold capture width is then easily obtained. Since atmospheric recombination involves very low energy electrons, the threshold capture widths are essential to the calculation of DR cross sections for the atmospheric species studied here. The approach described makes use of bound state computer codes already in use. A program that collects width matrix elements over CI wavefunctions for the initial and final states is described.

Guberman, S. L.↗

Infrared Spectroscopy of Matrix-Isolated Polycyclic Aromatic Nitrogen Heterocycles (PANHs)

The mid-infrared spectra of the nitrogen-containing heterocyclic polycyclic aromatic compounds 1-azabenz[a]-anthracene; 2-azabenz[a]anthracene; 1-azachrysene; 2-azachrysene; 4-azachrysene; 2-azapyrene, and 7,8 benzoquinoline in their neutral and cation forms were investigated. The spectra of these species isolated in an argon matrix have been measured. Band frequencies and intensities were tabulated and these data compared with spectra computed using density functional theory at the B3LYP level. The overall agreement between experiment and theory is quite good, in keeping with earlier results on homonuclear polycyclic aromatic hydrocarbons. The differences between the spectral properties of nitrogen bearing aromatics and non-substituted, neutral polycyclic aromatic hydrocarbons will be discussed.

Mattioda, A. L.↗

Inorganic Chlorine Partitioning in the Summer Lower Stratosphere: Modeled and Measured [ClONO2/HCl] During POLARIS

We examine inorganic chlorine (Cly) partitioning in the summer lower stratosphere using in situ ER-2 aircraft observations made during the Photochemistry of Ozone Loss in the Arctic Region in Summer (POLARIS) campaign. New steady state and numerical models estimate [ClONO2]/[HCl] using currently accepted photochemistry. These models are tightly constrained by observations with OH (parameterized as a function of solar zenith angle) substituting for modeled HO2 chemistry. We find that inorganic chlorine photochemistry alone overestimates observed [ClONO2]/[HCl] by approximately 55-60% at mid and high latitudes. On the basis of POLARIS studies of the inorganic chlorine budget, [ClO]/[ClONO2], and an intercomparison with balloon observations, the most direct explanation for the model-measurement discrepancy in Cly partitioning is an error in the reactions, rate constants, and measured species concentrations linking HCl and ClO (simulated [ClO]/[HCl] too high) in combination with a possible systematic error in the ER-2 ClONO2 measurement (too low). The high precision of our simulation (+/-15% 1-sigma for [ClONO2]/[HCl], which is compared with observations) increases confidence in the observations, photolysis calculations, and laboratory rate constants. These results, along with other findings, should lead to improvements in both the accuracy and precision of stratospheric photochemical models.

Voss, P. B.↗

Aromatic Diimides - Potential Dyes for Use in Smart Films and Fibers

New aromatic diimide fluorescent dyes have been prepared with potential for use as chemical sensors and in chromogenic polymers. These dyes have been designed to utilize excited state electron transfer reactions as the means for sensing chemical species. For example, an aniline en-dcapped anthryl diimides functions effectively as an "on-off" sensor for pH and the detection of phosphoryl halide based chemical warfare agents, such as Sarin. In the absence of analytes, fluorescence from this dye is completely quenched by excited state electron transfer from the terminal amines. Reaction of these amines inhibits electron transfer and activates the fluorescence of the dye. Another substituted anthryl diimide is presented with the capability to detect pH and nitroaromatic compounds, such as TNT. Films prepared by doping small amounts (less than 0.1 weight percent) of several of these dyes in polymers such as linear low density polyethylene exhibit thermochromism. At room temperature, these films fluoresce reddish-orange. Upon heating, the fluorescence turns green. This process is reversible cooling the films to room temperature restores the orange emission.

Meador, Michael A.↗

Generalized Fluid System Simulation Program

A general purpose program implemented on a computer analyzes steady state and transient flow in a complex fluid network, modeling phase changes, compressibility, mixture thermodynamics and external body forces such as gravity and centrifugal force. A preprocessor provides for the inter- active development of a fluid network simulation having nodes and branches. Mass, energy, and specie conservation equations are solved at the nodes, and momentum conservation equations are solved in the branches. Contained herein are subroutines for computing "real fluid" thermodynamic and thermophysical properties for 12 fluids, and a number of different source options are provided for model- ing momentum sources or sinks in the branches. The system of equations describing the fluid network is solved by a hybrid numerical method that is a combination of the Newton-Raphson and successive substitution methods. Application and verification of this invention are provided through an example problem, which demonstrates that the predictions of the present invention compare most reasonably with test data.

Alok Kumar Majumdar↗

Formation of Benzene in the Interstellar Medium

Polycyclic aromatic hydrocarbons and related species have been suggested to play a key role in the astrochemical evolution of the interstellar medium, but the formation mechanism of even their simplest building block-the aromatic benzene molecule-has remained elusive for decades. Here we demonstrate in crossed molecular beam experiments combined with electronic structure and statistical calculations that benzene (C6H6) can be synthesized via the barrierless, exoergic reaction of the ethynyl radical and 1,3- butadiene, C2H + H2CCHCHCH2 --> C6H6, + H, under single collision conditions. This reaction portrays the simplest representative of a reaction class in which aromatic molecules with a benzene core can be formed from acyclic precursors via barrierless reactions of ethynyl radicals with substituted 1,3-butadlene molecules. Unique gas-grain astrochemical models imply that this low-temperature route controls the synthesis of the very first aromatic ring from acyclic precursors in cold molecular clouds, such as in the Taurus Molecular Cloud. Rapid, subsequent barrierless reactions of benzene with ethynyl radicals can lead to naphthalene-like structures thus effectively propagating the ethynyl-radical mediated formation of aromatic molecules in the interstellar medium.

Jones, Brant M.↗

Cationic vinyl pyridine copolymers and products thereof

Quaternized, cross-linked, insoluble copolymers of unsubstituted and substituted vinyl pyridines and a dihalo organic compound are spontaneously formed at ambient temperature on mixing the two monomers in bulk, in solution or in suspension. The amount of cross-linking may be varied according to the composition and reaction conditions. The polymer product exhibits ion exchange capacity and undergoes a reversible color change from black at a pH above 7 to yellow at a pH below 7. The polymer may be formed in the presence of preformed polymers, substrates such as porous or impervious particles or films to deposit an ion exchange film in situ or on the surface of the substrate. The coated or resin impregnated substrate may be utilized for separation of anionic species from aqueous solution.

Rembaum, Alan↗

Improved Charge-Transfer Fluorescent Dyes

Improved charge-transfer fluorescent dyes have been developed for use as molecular probes. These dyes are based on benzofuran nuclei with attached phenyl groups substituted with, variously, electron donors, electron acceptors, or combinations of donors and acceptors. Optionally, these dyes could be incorporated as parts of polymer backbones or as pendant groups or attached to certain surfaces via self-assembly-based methods. These dyes exhibit high fluorescence quantum yields -- ranging from 0.2 to 0.98, depending upon solvents and chemical structures. The wavelengths, quantum yields, intensities, and lifetimes of the fluorescence emitted by these dyes vary with (and, hence, can be used as indicators of) the polarities of solvents in which they are dissolved: In solvents of increasing polarity, fluorescence spectra shift to longer wavelengths, fluorescence quantum yields decrease, and fluorescence lifetimes increase. The wavelengths, quantum yields, intensities, and lifetimes are also expected to be sensitive to viscosities and/or glass-transition temperatures. Some chemical species -- especially amines, amino acids, and metal ions -- quench the fluorescence of these dyes, with consequent reductions in intensities, quantum yields, and lifetimes. As a result, the dyes can be used to detect these species. Another useful characteristic of these dyes is a capability for both two-photon and one-photon absorption. Typically, these dyes absorb single photons in the ultraviolet region of the spectrum (wavelengths < 400 nm) and emit photons in the long-wavelength ultraviolet, visible, and, when dissolved in some solvents, near-infrared regions. In addition, these dyes can be excited by two-photon absorption at near-infrared wavelengths (600 to 800 nm) to produce fluorescence spectra identical to those obtained in response to excitation by single photons at half the corresponding wavelengths (300 to 400 nm). While many prior fluorescent dyes exhibit high quantum yields, solvent-polarity- dependent fluorescence behavior, susceptibility to quenching by certain chemical species, and/or two-photon fluorescence, none of them has the combination of all of these attributes. Because the present dyes do have all of these attributes, they have potential utility as molecular probes in a variety of applications. Examples include (1) monitoring curing and deterioration of polymers; (2) monitoring protein expression; (3) high-throughput screening of drugs; (4) monitoring such chemical species as glucose, amines, amino acids, and metal ions; and (5) photodynamic therapy of cancers and other diseases.

Meador, Michael↗

Relating FTS Catalyst Properties to Performance

During the reporting period June 23, 2011 to August 31, 2013, CAER researchers carried out research in two areas of fundamental importance to the topic of cobalt-based Fischer-Tropsch Synthesis (FTS): promoters and stability. The first area was research into possible substitute promoters that might be used to replace the expensive promoters (e.g., Pt, Re, and Ru) that are commonly used. To that end, three separate investigations were carried out. Due to the strong support interaction of γ-Al2O3 with cobalt, metal promoters are commonly added to commercial FTS catalysts to facilitate the reduction of cobalt oxides and thereby boost active surface cobalt metal sites. To date, the metal promoters examined have been those up to and including Group 11. Because two Group 11 promoters (i.e., Ag and Au) were identified to exhibit positive impacts on conversion, selectivity, or both, research was undertaken to explore metals in Groups 12 - 14. The three metals selected for this purpose were Cd, In, and Sn. At a higher loading of 25%Co on alumina, 1% addition of Cd, In, or Sn was found to-on average-facilitate reduction by promoting a heterogeneous distribution of cobalt consisting of larger lesser interacting cobalt clusters and smaller strongly interacting cobalt species. The lesser interacting species were identified in TPR profiles, where a sharp low temperature peak occurred for the reduction of larger, weakly interacting, CoO species. In XANES, the Cd, In, and Sn promoters were found to exist as oxides, whereas typical promoters (e.g., Re, Ru, Pt) were previously determined to exist in an metallic state in atomic coordination with cobalt. The larger cobalt clusters significantly decreased the active site density relative to the unpromoted 25%Co/Al2O3 catalyst. Decreasing the cobalt loading to 15%Co eliminated the large non-interacting species. The TPR peak for reduction of strongly interacting CoO in the Cd promoted catalyst occurred at a measurably lower temperature than in the unpromoted catalyst. Nevertheless, the Co clusters remained slightly larger, on average, in comparison with the unpromoted 15%Co/Al2O3 reference catalyst. None of the promoted catalysts (i.e., with Cd, In, or Sn) exhibited surface Co0 site densities higher than that of the unpromoted catalyst. In activity testing, the activities were even much lower than what was expected from the H2-TPD results. Two possible explanations were proposed: (1) the promoters may be located on the surfaces of cobalt particles, blocking surface Co0 but being able to desorb hydrogen or (2) the promoters may facilitate Co oxidation during FTS, as previously observed by Huffman and coworkers when K was added to cobalt catalysts.

Zirconia↗

Risk cross sections and their application to risk estimation in the galactic cosmic-ray environment

Radiation risk cross sections (i.e. risks per particle fluence) are discussed in the context of estimating the risk of radiation-induced cancer on long-term space flights from the galactic cosmic radiation outside the confines of the earth's magnetic field. Such quantities are useful for handling effects not seen after low-LET radiation. Since appropriate cross-section functions for cancer induction for each particle species are not yet available, the conventional quality factor is used as an approximation to obtain numerical results for risks of excess cancer mortality. Risks are obtained for seven of the most radiosensitive organs as determined by the ICRP [stomach, colon, lung, bone marrow (BFO), bladder, esophagus and breast], beneath 10 g/cm2 aluminum shielding at solar minimum. Spectra are obtained for excess relative risk for each cancer per LET interval by calculating the average fluence-LET spectrum for the organ and converting to risk by multiplying by a factor proportional to R gamma L Q(L) before integrating over L, the unrestricted LET. Here R gamma is the risk coefficient for low-LET radiation (excess relative mortality per Sv) for the particular organ in question. The total risks of excess cancer mortality obtained are 1.3 and 1.1% to female and male crew, respectively, for a 1-year exposure at solar minimum. Uncertainties in these values are estimated to range between factors of 4 and 15 and are dominated by the biological uncertainties in the risk coefficients for low-LET radiation and in the LET (or energy) dependence of the risk cross sections (as approximated by the quality factor). The direct substitution of appropriate risk cross sections will eventually circumvent entirely the need to calculate, measure or use absorbed dose, equivalent dose and quality factor for such a high-energy charged-particle environment.

NASA Discipline Radiation Health↗

A Generalized Fluid System Simulation Program to Model Flow Distribution in Fluid Networks

This paper describes a general purpose computer program for analyzing steady state and transient flow in a complex network. The program is capable of modeling phase changes, compressibility, mixture thermodynamics and external body forces such as gravity and centrifugal. The program's preprocessor allows the user to interactively develop a fluid network simulation consisting of nodes and branches. Mass, energy and specie conservation equations are solved at the nodes; the momentum conservation equations are solved in the branches. The program contains subroutines for computing "real fluid" thermodynamic and thermophysical properties for 33 fluids. The fluids are: helium, methane, neon, nitrogen, carbon monoxide, oxygen, argon, carbon dioxide, fluorine, hydrogen, parahydrogen, water, kerosene (RP-1), isobutane, butane, deuterium, ethane, ethylene, hydrogen sulfide, krypton, propane, xenon, R-11, R-12, R-22, R-32, R-123, R-124, R-125, R-134A, R-152A, nitrogen trifluoride and ammonia. The program also provides the options of using any incompressible fluid with constant density and viscosity or ideal gas. Seventeen different resistance/source options are provided for modeling momentum sources or sinks in the branches. These options include: pipe flow, flow through a restriction, non-circular duct, pipe flow with entrance and/or exit losses, thin sharp orifice, thick orifice, square edge reduction, square edge expansion, rotating annular duct, rotating radial duct, labyrinth seal, parallel plates, common fittings and valves, pump characteristics, pump power, valve with a given loss coefficient, and a Joule-Thompson device. The system of equations describing the fluid network is solved by a hybrid numerical method that is a combination of the Newton-Raphson and successive substitution methods. This paper also illustrates the application and verification of the code by comparison with Hardy Cross method for steady state flow and analytical solution for unsteady flow.

Majumdar, Alok↗

Nebular properties from far-infrared spectrosopy

We describe a semiempirical methodology-based on measurements of far-infrared (FIR) lines-that yields information on electron densities in regions where various ionic species exist, effective temperatures (T(sub eff)) for stars ionizing H II regions, and gas-phase heavy element abundances. Although this capability has long been available via optical data, the special features of FIR lines-relative insensitivity to extinction and electron temperature variations-extend the analysis ability. Several line ratios serve as diagnostics of electron density, N(sub e), probing different ionization conditions and different density regimes. The more N(sub e)-diagnostic observations made, the more reliable will be the deciphering of the actual variation in density throughout a nebula. A method to estimate T(sub eff) from the FIR (N III)/(N II) line ratio requires that the nebula be ionization bounded and that substantially all of the flux from the revevant lines be observed. However, to estimate T(sub eff) by a second method that uses the ratio of FIR (S III)/(O III) lines, an ionization-bounded nebula is a sufficient, but not necessary, condition. These restrictions are unnecessary for estimating densities and heavy element abundances. We show that a fairly general determination of metallicity, via the S/H ratio, may be made for H II regions with observations of just two lines-(S III) 19 micron and a hydrogen recombination line (or appropriate substitute). These techniques are applied to recent FIR data for the G333.6-0.2 H II region, including application to the recently measured (N II) 122 and 205 micron lines.

Rubin, Robert H.↗

Structural evolution, electrochemical kinetic properties, and stability of A-site doped perovskite Sr(1-x)Yb(x)CoO(3-δ)

Mixed ionic and electronic conducting (MIEC) perovskite SrCoO(3-δ) is a widely studied (electro)catalyst for the oxygen reduction reaction (ORR) and possesses different crystal structures at different temperatures. These temperature dependent phase transitions significantly impact the ordering of oxygen vacancies and electrochemical kinetic properties as well as the reliability of the related devices. Some of the crystal structures formed, e.g. hexagonal phases, turn out to be almost impermeable to oxygen gas. Therefore, it is important to stabilize the crystal structure of SrCoO(3-δ) that favors the ORR over a wide temperature range. Herein, the partial substitution of the A-site Sr with Yb is systematically studied, including synthesis, characterization and analysis of structural evolution, electrochemical kinetic properties, thermal stability, and stability in a CO2-containing atmosphere. The results indicate that Sr(0.90)Yb(0.10)CoO(3-δ) is able to stabilize the tetragonal crystal structure with less ordered oxygen vacancies, leading to polarization resistances of 0.051, 0.115 and 0.272 U sq.cm at 750, 700 and 650 °C, respectively, on symmetrical cells. Sr(0.90)Yb(0.10)CoO(3-δ) demonstrates a very stable surface oxygen vacancy distribution and electronic structure near oxygen vacancies but dissociation of adsorbed oxygen molecules into atomic oxygen is affected by surface Sr segregation, and polarization resistance degradation is mainly induced by surface Sr segregation. Furthermore, Sr(0.90)Yb(0.10)CoO(3-δ) exhibits excellent thermal stability as well as excellent recovery stability and improved polarization performance after a few pure air/CO2-containing air treatment cycles at 700 °C. However, a hysteresis behavior of polarization performance is observed at 650 °C during gas cycling treatment, which may cause long-term degradation of the Sr(0.90)Yb(0.10)CoO(3-δ) electrode. The different polarization behaviors during gas cycling treatment are induced by different sensitivities of the formed surface strontium carbonate and chemisorbed surface oxo-carbonaceous species to different operating temperatures.

electrochemical kinetic↗