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At least 919 records · Page 51

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NASA NTRS1993

Is ligation the only solution to the pyrophosphate problem?

Pyrophosphate linkages are easily formed during the nonenzymatic oligomerization of activated nucleotides. They often form `caps' which terminate an oligonucleotide with a 5'-5' pyrophosphate. Owing to their structural resemblance to the intermediates in enzymatic ligation reactions, it has been suggested that pyrophosphate caps might have been capable of acting as activating groups in chain elongation processes. We argue that an alternative possibility would have been the specific hydrolysis of pyrophosphates.

Visscher, J.↗

NASA NTRS1993

Applicability of PM3 to transphosphorylation reaction path: Toward designing a minimal ribozyme

A growing body of evidence shows that RNA can catalyze many of the reactions necessary both for replication of genetic material and the possible transition into the modern protein-based world. However, contemporary ribozymes are too large to have self-assembled from a prebiotic oligonucleotide pool. Still, it is likely that the major features of the earliest ribozymes have been preserved as molecular fossils in the catalytic RNA of today. Therefore, the search for a minimal ribozyme has been aimed at finding the necessary structural features of a modern ribozyme (Beaudry and Joyce, 1990). Both a three-dimensional model and quantum chemical calculations are required to quantitatively determine the effects of structural features of the ribozyme on the reaction it catalyzes. Using this model, quantum chemical calculations must be performed to determine quantitatively the effects of structural features on catalysis. Previous studies of the reaction path have been conducted at the ab initio level, but these methods are limited to small models due to enormous computational requirements. Semiempirical methods have been applied to large systems in the past; however, the accuracy of these methods depends largely on a simple model of the ribozyme-catalyzed reaction, or hydrolysis of phosphoric acid. We find that the results are qualitatively similar to ab initio results using large basis sets. Therefore, PM3 is suitable for studying the reaction path of the ribozyme-catalyzed reaction.

Manchester, John I.↗

NASA NTRS1995

The fate of atmospheric phosgene and the stratospheric chlorine loadings of its parent compounds: CCl4, C2Cl4, C2HCL3, CH3CCl3, and CHCl3

A study of the tropospheric and stratospheric cycles of phosgene is carried out to determine its fate and ultimate role in controlling the ozone depletion potentials of its parent compounds. Tropospheric phosgene is produced from the OH-initiated oxidation of C2Cl4, CH3CCl3, CHCl3, and C2HCl3. Simulations using a two-dimensional model indicate that these processes produce about 90 pptv/yr of tropospheric phosgene with an average concentration of about 18 pptv, in reasonable agreement with observations. We estimate a residence time of about 70 days for tropospheric phosgene, with the vast majority being removed by hydrolysis in cloudwater. Only about 0.4% of the phosgene produced in the troposphere avoids wet removal and is transported to the stratosphere, where its chlorine can be released to participate in the catalytic destruction of ozone. Stratospheric phosgene is produced from the photochemical degradation of CCl4, C2Cl4, CHCl3, and CH3CCl3 and is removed by photolysis and downward transport to the troposphere. Model calculations, in good agreement with observations, indicate that these processes produce a peak stratospheric concentration of about 25-30 pptv at an altitude of about 25 km. In contrast to tropospheric phosgene, stratospheric phosgene is found to have a lifetime against photochemical removal of the order of years. As a result, a significant portion of the phosgene that is produced in the stratosphere is ultimately returned to the troposphere, where it is rapidly removed by clouds. This phenomenon effectively decreases the amount of reactive chlorine injected into the stratosphere and available for ozone depletion from phosgene's parent compounds. A similar phenomenon due to the downward transport of stratospheric COFCl produced from CFC-11 is estimated to cause a 7% decrease in the amount of reactive chlorine injected into the stratosphere from this compound. Our results are potentially sensitive to a variety of parameters, most notably the rate of reaction of phosgene with sulfate aerosols. However, on the basis of the observed vertical distribution of COCl2, we estimate that the reaction of COCl2 with sulfate aerosol most likely has a gamma less than 5 x 10(exp -5) and, as a result, has a negligible impact on the stratospheric chlorine loadings of the phosgene parent compounds.

Kindler, T. P.↗

NASA NTRS1993

In situ measurements of ClO at mid-latitudes: Is there an effect from Mt. Pinatubo?

Observations of ClO from 20 to 60 deg N made before and after the eruption of Mt. Pinatubo are compared for changes which may result from increased sulfate aerosol surface area. Using ozone as a vertical coordinate and examining data at similar latitudes and seasons, elevated abundances of ClO are found at low latitudes (20 to 30 deg N), an effect which decreases with increasing latitude. For the flights compared, there appear to be no differences, within the uncertainty of the measurements, at latitudes poleward of 40 deg N. These results are consistent with the idea that the hydrolysis of N2O5 on sulfate aerosols becomes saturated at moderate aerosol loadings.

Avallone, L. M.↗

NASA NTRS1994

The distribution of hydrogen, nitrogen, and chlorine radicals in the lower stratosphere: Implications for changes in O3 due to emission of NO(y) from supersonic aircraft

In situ measurements of hydrogen, nitrogen, and chlorine radicals obtained in the lower statosphere during SPADE are compared to results from a photochemical model that assimilates measurements of radical precursors and environmental conditions. Models allowing for heterogeneous hydrolysis of N2O5 agree well with measured concentrations of NO and ClO, but concentrations of HO2 and OH are underestimated by 10 to 25%, concentrations of NO2 are overestimated by 10 to 30%, and concentrations of HCl are overestimated by a factor of 2. Discrepancies for (OH) and (HO2) are reduced if we allow for higher yields of O((1)D) from O2 photolysis and for heterogeneous production of HNO2. The data suggest more efficent catalytic removal of O3 by hydrogen and halogen radicals relative to nitrogen oxide radicals than predicted by models using recommendend rates and cross sections. Increased in (O3) in the lower stratosphere may be larger in response to inputs of NO(y) from supersonic aircraft than estimated by current assessment models.

Salawitch, R. J.↗

NASA NTRS1994

The diurnal variation of hydrogen, nitrogen, and chlorine radicals: Implications for the heterogeneous production of HNO2

In situ measurements of hydrogen, nitrogen, and chlorine radicals obtained through sunrise and sunset in the lower statosphere during SPADE are compared to results from a photochemical model constrained by observed concentrations of radical precursors and environmental conditions. Models allowing for heteogeneous hydrolysis of N2O5 on sulfate aerosols agree with measured concentrations of NO, NO2, and ClO throughout the day, but fail to account for high concentrations of OH and HO2 observed near sunrise and sunset. The morning burst of (OH) and (HO2) coincides with the rise of (NO) from photolysis of NO2, suggesting a new source of HO(x) that photolyzes in the near UV (350 to 400 nm) spectral region. A model that allow for the heterogeneous production of HNO2 results in an excellent simulation of the diurnal variations of (OH) and (HO2).

Salawitch, R. J.↗

NASA NTRS1995

Evidence for organic synthesis in high temperature aqueous media - facts and prognosis

Hydrothermal systems are common along the active tectonic areas of the earth. Potential sites being studied for organic matter alteration and possible organic synthesis are spreading ridges, off-axis systems, back-arc activity, hot spots, volcanism, and subduction. Organic matter alteration, primarily reductive and generally from immature organic detritus, occurs in these high temperature and rapid fluid flow hydrothermal regimes. Hot circulating water (temperature range - warm to greater than 400 C) is responsible for these molecular alterations, expulsion and migration. Compounds that are obviously synthesized are minor components because they are generally masked by the pyrolysis products formed from contemporary natural organic precursors. The reactivity of organic compounds in hot water (200-350 C) has been studied in autoclaves, and supercritical water as a medium for chemistry has also been evaluated. This high temperature aqueous organic chemistry and the strong reducing conditions of the natural systems suggest this as an important route to produce organic compounds on the primitive earth. Thus a better understanding of the potential syntheses of organic compounds in hydrothermal systems will require investigations of the chemistry of condensation, autocatalysis, catalysis and hydrolysis reactions in aqueous mineral buffered systems over a range of temperatures from warm to greater than 400 C.

Simoneit, Bernd R. T.↗

NASA NTRS1995

Environmentally Sound Processing Technology: JANNAF Safety and Environmental Protection Subcommittee and Propellant Development and Characterization Subcommittee Joint Workshop

Topics covered include: Risk assessment of hazardous materials, Automated systems for pollution prevention and hazardous materials elimination, Study design for the toxicity evaluation of ammonium perchlorate, Plasma sprayed bondable stainless surface coatings, Development of CFC-free cleaning processes, New fluorinated solvent alternatives to ozone depleting solvents, Cleaning with highly fluorinated liquids, Biotreatment of propyleneglycol nitrate by anoxic denitrification, Treatment of hazardous waste with white rot fungus, Hydrothermal oxidation as an environmentally benign treatment technology, Treatment of solid propellant manufacturing wastes by base hydrolysis, Design considerations for cleaning using supercritical fluid technology, and Centrifugal shear carbon dioxide cleaning.

Pickett, Lorri A.↗

NASA NTRS1997

New Approaches to Waterproofing of Space Shuttle Insulating Materials

Future reusable space vehicles will be in service much more frequently than current space shuttles. Therefore, rapid reconditioning of spacecraft will be required. Currently, the waterproofing of space shuttles after each re-entry takes 72 hours and requires substantial labor. In addition, the currently used waterproofing reagent, DiMethylEthoxySilane (DMES), is considered toxic, and ethanol fumes are released during its hydrolytic activation. Consequently, a long time period, which is not acceptable for future operations, is needed to ensure that 0 the excess volatile compounds are removed before further maintenance of the space vehicle can be performed. The objective of this project was to assist NASA Ames in finding improved waterproofing systems by identifying suitable waterproofing agents that can be applied by vapor phase deposition and will be less toxic, bond more rapidly to the insulation material surface, and potentially have higher thermal stability than the DMES system. Several approaches to achieve faster waterproofing with less toxicity were assessed using the following alternatives: Reactive volatile compounds that are rapidly deposited by chemical bonding at the surface and leave no toxic volatiles. Reactive reagents that are the least toxic. Nonvolatile reagents that are very reactive and bond strongly to the insulating material surface. Three specific types of potential reagents were chosen for evaluation in this project: 1. Volatile reagents with Si-Cl functional groups for vapor deposition 2. Volatile reagents with Si-H functional groups for vapor deposition 3. Nonvolatile oligomeric or polymeric reactive siloxanes that are assumed to have higher thermal stability and/or strong bonding to the insulating material. The chemistry involved in the project was targeted at the generation of intermediates having reactive Si-OH bonds for the formation of either volatile species or polymeric species that bond rapidly to the surface and also cure rapidly. We focused on two chemical reactions@-hydrolysis of Si-Cl bonds and catalytic dehydrocoupling of Si-H bonds.

Blum, Yigal D.↗

NASA NTRS1997

A Simple Procedure for Constructing 5'-Amino-Terminated Oligodeoxynucleotides in Aqueous Solution

A rapid method for the synthesis of oligodeoxynucleotides (ODNs) terminated by 5'-amino-5'-deoxythymidine is described. A 3'-phosphorylated ODN (the donor) is incubated in aqueous solution with 5'-amino- 5'-deoxythymidine in the presence of N-(3-dimethylaminopropyl)-)N'-ethylcarbodiimide hydrochloride (EDC), extending the donor by one residue via a phosphoramidate bond. Template- directed ligation of the extended donor and an acceptor ODN, followed by acid hydrolysis, yields the acceptor ODN extended by a single 5'-amino-5'-deoxythymidine residue at its 5'terminus.

Bruick, Richard K.↗

NASA NTRS1994

The Diurnal Variation of Hydrogen, Nitrogen, and Chlorine Radicals: Implications for the Heterogeneous Production of HNO2

In situ measurements of hydrogen, nitrogen, and chlorine radicals obtained through sunrise and sunset in the lower stratosphere during SPADE are compared to results from a photochemical model constrained by observed concentrations of radical precursors and environmental conditions. Models allowing for heterogeneous hydrolysis of N205 on sulfate aerosols agree with measured concentrations of NO, NO2, and ClO throughout the day, but fail to account for high concentrations of OH and H02 observed near sunrise and sunset. The morning burst of [OH] and [HO2] coincides with the rise of [NO] from photolysis of N02, suggesting a new source of HO, that photolyzes in the near UV (350 to 400 nm) spectral region. A model that allows for the heterogeneous production of HN02 results in an excellent simulation of the diurnal variations of [OH] and [HO2].

Salawitch, R. J.↗

NASA NTRS1993

In Situ Measurements of CLO at Mid-Latitudes: Is there an Effect from Mt. Pinatubo?

Avallone, L. M.↗

NASA NTRS1994

The Distribution of Hydrogen, Nitrogen, and Chlorine Radicals in the Lower Stratosphere: Implications for Changes in O3 due to Emission of NO(y) from Supersonic Aircraft

In situ measurements of hydrogen, nitrogen, and chlorine radicals obtained in the lower stratosphere during the Stratospheric Photochemistry, Aerosols and Dynamics Expedition (SPADE) are compared to results from a photochemical model that assimilates measurements of radical precursors and environmental conditions. Models allowing for heterogeneous hydrolysis of N2O5 agree well with measured concentrations of NO and ClO, but concentrations of HO2 and OH are underestimated by 10 to 25%, concentrations of NO2 are overestimated by 10 to 30%, and concentrations of HCl are overestimated by a factor of 2. Discrepancies for [OH] and [HO2] are reduced if we allow for higher yields of O(sup 1)D) from 03 photolysis and for heterogeneous production of HNO2. The data suggest more efficient catalytic removal of O3 by hydrogen and halogen radicals relative to nitrogen oxide radicals than predicted by models using recommended rates and cross sections. Increases in [O3] in the lower stratosphere may be larger in response to inputs of NO(sub y) from supersonic aircraft than estimated by current assessment models.

Salawitch, R. J.↗

NASA NTRS1997

Dimerization in Highly Concentrated Solutions of Phosphoimidazolide Activated Mononucleotides

Phosphoimidazolide activated ribomononucleotides (*pN) are useful substrates for the non-enzymatic synthesis of polynucleotides. However, dilute neutral aqueous solutions of *pN typically yield small amounts of dimers and traces of polymers; most of *pN hydrolyzes to yield nucleoside 5'-monophosphate. Here we report the self-condensation of nucleoside 5'-phosphate 2- methylimidazolide (2-MeImpN with N = cytidine, uridine or guanosine) in the presence of Mg2(+) in concentrated solutions, such as might have been found in an evaporating lagoon on prebiotic Earth. The product distribution indicates that oligomerization is favored at the expense of hydrolysis. At 1.0 M, 2-MelmpU and 2-MelmpC produce about 65% of oligomers including 4% of the 3',5'-Iinked dimer. Examination of the product distribution of the three isomeric dimers in a self-condensation allows identification of reaction pathways that lead to dimer formation. Condensations in a concentrated mixture of all three nucleotides (U,C,G mixtures) is made possible by the enhanced solubility of 2-MeImpG in such mixtures. Although percent yield of intemucleotide linked dimers is enhanced as a function of initial monomer concentration, pyrophosphate dimer yields remain practically unchanged at about 20% for 2-MelmpU, 16% for 2-MeImpC and 25% of the total pyrophosphate in the U,C,G mixtures. The efficiency by which oligomers are produced in these concentrated solutions makes the evaporating lagoon scenario a potentially interesting medium for the prebiotic synthesis of dimers and short RNAs.

Kanavarioti, Anastassia↗

NASA NTRS1996

Synthesis of long Prebiotic Oligomers on Mineral Surfaces

Most theories of the origin of biological organization assume that polymers with lengths in the range of 30-60 monomers are needed to make a genetic system viable. But it has not proved possible to synthesize plausibly prebiotic polymers this long by condensation in aqueous solution, because hydrolysis competes with polymerization. The potential of mineral surfaces to facilitate prebiotic polymerization was pointed out long ago. Here we describe a system that models prebiotic polymerization by the oligomerization of activated monomers -both nucleotides and amino acids. We find that whereas the reactions in solution produce only short oligomers (the longest typically being a 10-mer), the presence of mineral surfaces (montmorillonite for nucleotides, illite and hydroxylapatite for amino adds) induces the formation of oligomers up to 55 monomers long. These are formed by successive "feedings" with the monomers; polymerization takes place on the mineral surfaces in a manner akin to solid-phase synthesis of biopolymers.

Ferris, James P.↗

NASA NTRS1996

Prebiotic Synthesis of Diaminopyrimidine and Thiocytosine

The reaction of guanidine hydrochloride with cyanoacetaldehyde gives high yields (40-85%) of 2,4-diaminopyrimidine under the concentrated conditions of a drying lagoon model of prebiotic synthesis, in contrast to the low yields previously obtained under more dilute conditions. The prebiotic source of cyanoacetaldehyde, cyanoacetylene, is produced from electric discharges under reducing conditions. The effect of pH and concentration of guanidine hydrochloride on the rate of synthesis and yield of diaminopyrimidine were investigated, as well as the hydrolysis of diaminopyrimidine to cytosine, isocytosine, and uracil. Thiourea also reacts with cyanoacetaldehyde to give 2-thiocytosine, but the pyrimidine yields are much lower than with guanidine hydrochloride or urea. Thiocytosine hydrolyzes to thiouracil and cytosine and then to uracil. This synthesis would have been a significant prebiotic source of 2-thiopyrimidines and 5-substituted derivatives of thiouracil, many of which occur in tRNA. The applicability of these results to the drying lagoon model of prebiotic synthesis was tested by dry-down experiments where dilute solutions of cyanoacetaldehyde, guanidine hydrochloride, and 0.5 M NaCl were evaporated over varying periods of time. The yields of diaminopyrimidine varied from 1 to 7%. These results show that drying lagoons and beaches may have been major sites of prebiotic syntheses.

Robertson, Michael P.↗

NASA NTRS1995

Are Polyphosphates or Phosphate Esters Prebiotic Reagents?

It is widely held that there was a phosphate compound in prebiotic chemistry that played the role of adenosine triphosphate and that the first living organisms had ribose-phosphate in the backbone of their genetic material. However, there are no known efficient prebiotic synthesis of high-energy phosphates or phosphate esters. We review the occurrence of phosphates in nature, the efficiency of the volcanic synthesis of P4O10, the efficiency of polyphosphate synthesis by heating phosphate minerals under geological conditions, and the use of high-energy organic compounds such as cyanamide or hydrogen cyanide. These are shown to be inefficient processes especially when the hydrolysis of the polyphosphates is taken into account. For example, if a whole atmosphere of methane or carbon monoxide were converted to cyanide which somehow synthesized polyphosphates quantitatively, the polyphosphate concentration in the ocean would still have been insignificant. We also attempted to find more efficient high-energy polymerizing agents by spark discharge syntheses, but without success. There may still be undiscovered robust prebiotic syntheses of polyphosphates, or mechanisms for concentrating them, but we conclude that phosphate esters may not have been constituents of the first genetic material. Phosphoanhydrides are also unlikely as prebiotic energy sources.

Keefe, Anthony D.↗

NASA NTRS1996

Was Ferrocyanide a Prebiotic Reagent?

Hydrogen cyanide is the starting material for a diverse array of prebiotic syntheses, including those of amino acids and purines. Hydrogen cyanide also reacts with ferrous ions to give ferrocyanide, and so it is possible that ferrocyanide was common in the early ocean. This can only be true if the hydrogen cyanide concentration was high enough and the rate of reaction of cyanide with ferrous ions was fast enough. We show experimentally that the rate of formation of ferrocyanide is rapid even at low concentrations of hydrogen cyanide in the pH range 6-8, and therefore an equilibrium calculation is valid. The equilibrium concentrations of ferrocyanide are calculated as a function of hydrogen cyanide concentration, pH and temperature. The steady state concentration of hydrogen cyanide depends on the rate of synthesis by electric discharges and ultraviolet light and the rate of hydrolysis, which depends on pH and temperature. Our conclusions show that ferrocyanide was a major species in the prebiotic ocean only at the highest production rates of hydrogen cyanide in a strongly reducing atmosphere and at temperatures of 0 C or less, although small amounts would have been present at lower hydrogen cyanide production rates. The prebiotic application of ferrocyanide as a source of hydrated electrons, as a photochemical replication process, and in semi-permeable membranes is discussed.

Keefe, Anthony D.↗