RETRACTED: Metal Catalysis Acting on Nitriles in Early Earth Hydrothermal Systems
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Miranda Sturtz↗
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Macromolecular recognition: Structural aspects of the origin of the genetic system
Theoretical simulation of prebiotic chemical processes is an invaluable tool for probing the phenomenon of evolution of life. Using computational and modeling techniques and guided by analogies from present day systems we, seek to understand the emergence of genetic apparatus, enzymatic catalysis and protein synthesis under prebiotic conditions. In one possible scenario, the RNA enzymatic reaction plays a key role in the emergence of the self-replicating and offers a clue to the onset of enzymatic catalysis prior to the existence of the protein biosynthetic machinery. Our ultimate goal is to propose a simple RNA segment which contains the specificity and catalytic activity of the contemporary RNA enzyme and which could emerge in a primordial chemical environment. To understand the mechanism of ribozyme catalyzed reactions, ab initio and semi-empirical (ZINDO) programs were used to investigate the reaction path of transphosphorylation. A special emphasis was placed on the possible catalytic and structural roles played by the coordinated magnesium cation. Both the inline and adjacent mechanisms of transphosphorylation have been studied. Another important aspect of this reaction is the identity of the functional groups which are essential for the acid base catalysis. The structural characteristics of the target helices, particularly a possible role of G center dot T pair, is under examination by molecular dynamics (MD) simulation technique. Modeling of the ancestral aminoacyl-tRNA synthetases (aRS) may provide important clues to the emergence of the genetic code and the protein synthetic machinery. Assuming that the catalytic function evolved before the elements of specific recognition of a particular amino acid, we are exploring the minimal structural requirements for the catalysis of tRNA aminoacylation. The molecular modeling system SYBYL was used for this study based on the high resolution crystallographic structures of the present day tyrosyl-adenylate:tyrRS and tRNA(Gln): ATP:glnRS complexes. The trinucleotide CCA of the 3'-end tRNA is placed into the active site pocket of tyrRS, based on the scheme of interaction between tRNA(Gln) and glnRS, and upon the stereochemistry of the tyrRS:tRNA:Tyr-AMP transition state. This provides a model of the non-specific recognition of a tRNA's 3'-end by an aRS, which might be similar to that of the ancestral aRS's. In the next step, modeling of the rest of the acceptor stem of tRNA (Tyr) with tyrRS is carried out.
Rein, Robert↗
Analysis of Aerothermal Heating Over Reusable Single-Stage to Orbit Vehicles
Using the General Aerodynamic Simulation Program (GASP) with finite-rate surface catalysis and radiative equilibrium surface temperature conditions, a computational study has been conducted to predict three-dimensional aero-convective heating over the proposed reusable single-stage to orbit vehicles. The solutions for three basic classes of usable single-stage-to-orbit vehicles, including wing body, lifting body and vertical lander, are presented and compared to provide information for vehicle design. The free stream conditions used in this study occur at an altitude of 57.5 km, ambient density of 4.129e-4 kg/cubic m, and velocity of 4,849 m/s. The convective heating over the vehicle surface in both laminar and turbulent flow regimes were computed. The Baldwin-Lomax algebraic model with a modified van Driest damping factor was applied in the turbulent flow calculations. A bifurcation model which guarantees the conservation of mass diffusive fluxes was adopted to account for the multi-species mass diffusion. The effects of turbulence and surface catalysis on the surface heating are discussed in detail The solutions indicate the degree of oxygen dissociation over the leeward side is sensitive to the shape of vehicle body. Predicted convective heating over the entire surface of lifting body is strongly affected by the presence of surface catalysis. For wing body and vertical lander, the surface catalysis effect does not appear to be important in the far downstream region, and turbulence is the dominant effect on the heating prediction in this region.
Chen, Y. K.↗
Reacting viscous-shock-layer solutions with multicomponent diffusion and mass injection
Numerical solutions of the viscous-shock-layer equation where the chemistry is treated as being either frozen, equilibrium, or nonequilibrium are presented. Also the effects of the diffusion model, surface catalysis, and mass injection on surface transport and flow parameters are considered. The flow is treated as a mixture of five inert and thermally perfect species. The viscous-shock-layer equations are solved by using an implicit-difference scheme. All calculations are for hyperboloids with included angles of 20 and 45. The flight conditions are those for various altitudes and velocities in the earth's atmosphere. Data are presented to show the effects of the chemical models; diffusion models; surface catalysis; and mass injection of air on heat transfer; skin friction; shock standoff distance; wall pressure distribution; and tangential velocity, temperature, and species profiles. The results show that an equilibrium analysis can substantially overpredict the heat-transfer rates for flow conditions experienced by earth-orbital entry vehicles. Moreover, at such conditions surface catalysis significantly influences heat-transfer and flow-field properties. If a binary rather than a multicomponent diffusion model is assumed, negligible errors in most flow properties result. Quantitative results are presented that show the effect of mass injection on flow properties within and downstream of the injection region.
Moss, J. N.↗
Heterogeneous atmospheric chemistry
The present conference on heterogeneous atmospheric chemistry considers such topics concerning clusters, particles and microparticles as common problems in nucleation and growth, chemical kinetics, and catalysis, chemical reactions with aerosols, electron beam studies of natural and anthropogenic microparticles, and structural studies employing molecular beam techniques, as well as such gas-solid interaction topics as photoassisted reactions, catalyzed photolysis, and heterogeneous catalysis. Also discussed are sulfur dioxide absorption, oxidation, and oxidation inhibition in falling drops, sulfur dioxide/water equilibria, the evidence for heterogeneous catalysis in the atmosphere, the importance of heterogeneous processes to tropospheric chemistry, soot-catalyzed atmospheric reactions, and the concentrations and mechanisms of formation of sulfate in the atmospheric boundary layer.
Schryer, D. R.↗
Theoretical study of the design of a catalyst for para to ortho hydrogen conversion
The theory of Petzinger and Scalapino (1973) was thoroughly reviewed, and all of the basic equations for paramagnetic para to ortho hydrogen catalysis re-derived. There are only a few minor phase errors and errors of omission in the description of the theory. Three models (described by Petzinger and Scalapino) for the rate of para to ortho H2 catalysis were worked out, and uniform agreement obtained to within a constant factor of 2 pi. The analytical methods developed in the course of this study were then extended to two new models, which more adequately describe the process of surface catalysis including transfer of hydrogen molecules onto and off of the surface. All five equations for the para to ortho catalytic rate of conversion are described. The two new equations describe the catalytic rate for these models: H2 on the surface is a 2-D gas with lifetime tau; and H2 on the surface is a 2-D liquid undergoing Brownian motion (diffusion) with surface lifetime tau.
Coffman, Robert E.↗
Thermal coatings for titanium-aluminum alloys
Titanium aluminides and titanium alloys are candidate materials for use in hot structure and heat-shield components of hypersonic vehicles because of their good strength-to-weight characteristics at elevated temperature. However, in order to utilize their maximum temperature capability, they must be coated to resist oxidation and to have a high total remittance. Also, surface catalysis for recombination of dissociated species in the aerodynamic boundary layer must be minimized. Very thin chemical vapor deposition (CVD) coatings are attractive candidates for this application because of durability and very light weight. To demonstrate this concept, coatings of boron-silicon and aluminum-boron-silicon compositions were applied to the titanium-aluminides alpha2 (Ti-14Al-21Nb), super-alpha2 (Ti-14Al-23-Nb-2V), and gamma (Ti-33Al-6Nb-1Ta) and to the titanium alloy beta-21S (Ti-15Mo-3Al-3Nb-0.2Si). Coated specimens of each alloy were subjected to a set of simulated hypersonic vehicle environmental tests to determine their properties of oxidation resistance, surface catalysis, radiative emittance, and thermal shock resistance. Surface catalysis results should be viewed as relative performance only of the several coating-alloy combinations tested under the specific environmental conditions of the LaRC Hypersonic Materials Environmental Test System (HYMETS) arc-plasma-heated hypersonic wind tunnel. Tests were also conducted to evaluate the hydrogen transport properties of the coatings and any effects of the coating processing itself on fatigue life of the base alloys. Results are presented for three types of coatings, which are as follows: (1) a single layer boron silicon coating, (2) a single layer aluminum-boron-silicon coating, and (3) a multilayer coating consisting of an aluminum-boron-silicon sublayer with a boron-silicon outer layer.
Cunnington, George R.↗
Isolation of novel ribozymes that ligate AMP-activated RNA substrates
BACKGROUND: The protein enzymes RNA ligase and DNA ligase catalyze the ligation of nucleic acids via an adenosine-5'-5'-pyrophosphate 'capped' RNA or DNA intermediate. The activation of nucleic acid substrates by adenosine 5'-monophosphate (AMP) may be a vestige of 'RNA world' catalysis. AMP-activated ligation seems ideally suited for catalysis by ribozymes (RNA enzymes), because an RNA motif capable of tightly and specifically binding AMP has previously been isolated. RESULTS: We used in vitro selection and directed evolution to explore the ability of ribozymes to catalyze the template-directed ligation of AMP-activated RNAs. We subjected a pool of 10(15) RNA molecules, each consisting of long random sequences flanking a mutagenized adenosine triphosphate (ATP) aptamer, to ten rounds of in vitro selection, including three rounds involving mutagenic polymerase chain reaction. Selection was for the ligation of an oligonucleotide to the 5'-capped active pool RNA species. Many different ligase ribozymes were isolated; these ribozymes had rates of reaction up to 0.4 ligations per hour, corresponding to rate accelerations of approximately 5 x10(5) over the templated, but otherwise uncatalyzed, background reaction rate. Three characterized ribozymes catalyzed the formation of 3'-5'-phosphodiester bonds and were highly specific for activation by AMP at the ligation site. CONCLUSIONS: The existence of a new class of ligase ribozymes is consistent with the hypothesis that the unusual mechanism of the biological ligases resulted from a conservation of mechanism during an evolutionary replacement of a primordial ribozyme ligase by a more modern protein enzyme. The newly isolated ligase ribozymes may also provide a starting point for the isolation of ribozymes that catalyze the polymerization of AMP-activated oligonucleotides or mononucleotides, which might have been the prebiotic analogs of nucleoside triphosphates.
NASA Discipline Exobiology↗
Montmorillonite, oligonucleotides, RNA and origin of life
Na-montmorillonite prepared from Volclay by the titration method facilitates the self-condensation of ImpA, the 5'-phosphorimidazolide derivative of adenosine. As was shown by AE-HPLC analysis and selective enzymatic hydrolysis of products, oligo(A)s formed in this reaction are 10 monomer units long and contain 67% 3',5'-phosphodiester bonds (Ferris and Ertem, 1992a). Under the same reaction conditions, 5'-phosphorimidazolide derivatives of cytidine, uridine and guanosine also undergo self-condensation producing oligomers containing up to 12-14 monomer units for oligo(C)s to 6 monomer units for oligo(G)s. In oligo(C)s and oligo(U)s, 75-80% of the monomers are linked by 2',5'-phosphodiester bonds. Hexamer and higher oligomers isolated from synthetic oligo(C)s formed by montmorillonite catalysis, which contain both 3',5'- and 2',5'-linkages, serve as catalysts for the non-enzymatic template directed synthesis of oligo(G)s from activated monomer 2-MeImpG, guanosine 5'-phospho-2-methylimidazolide (Ertem and Ferris, 1996). Pentamer and higher oligomers containing exclusively 2',5'-linkages, which were isolated from the synthetic oligo(C)s, also serve as templates and produce oligo(G)s with both 2',5'- and 3',5'-phosphodiester bonds. Kinetic studies on montmorillonite catalyzed elongation rates of oligomers using the computer program SIMFIT demonstrated that the rate constants for the formation of oligo(A)s increased in the order of 2-mer < 3-mer < 4-mer ... < 7-mer (Kawamura and Ferris, 1994). A decameric primer, dA(pdA)8pA bound to montmorillonite was elongated to contain up to 50 monomer units by daily addition of activated monomer ImpA to the reaction mixture (Ferris, Hill and Orgel, 1996). Analysis of dimer fractions formed in the montmorillonite catalyzed reaction of binary and quaternary mixtures of ImpA, ImpC, 2-MeImpG and ImpU suggested that only a limited number of oligomers could have formed on the primitive Earth rather than equal amounts of all possible isomers (Ertem and Ferris, 2000). Formation of phosphodiester bonds between mononucleotides by montmorillonite catalysis is a fascinating discovery, and a significant step forward in efforts to find out how the first RNA-like oligomers might have formed in the course of chemical evolution. However, as has been pointed out in several publications, these systems should be regarded as models rather than a literal representation of prebiotic chemistry (Orgel, 1998; Joyce and Orgel, 1999; Schwartz, 1999).
RNA/chemical synthesis↗
Polymer degradation rate control of hybrid rocket combustion
Polymer degradation to small fragments is treated as a rate controlling step in hybrid rocket combustion. Both numerical and approximate analytical solutions of the complete energy and polymer chain bond conservation equations for the condensed phase are obtained. Comparison with inert atmosphere data is very good. It is found that the intersect of curves of pyrolysis rate versus interface temperature for hybrid combustors, with the thermal degradation theory, falls at a pyrolysis rate very close to that for which a pressure dependence begins to be observable. Since simple thermal degradation cannot give sufficient depolymerization at higher pyrolysis rates, it is suggested that oxidative catalysis of the process occurs at the surface, giving a first order dependence on reactive species concentration at the wall. Estimates of the ratio of this activation energy and interface temperature are in agreement with best fit procedures for hybrid combustion data. Requisite active species concentrations and flux are shown to be compatible with turbulent transport. Pressure dependence of hybrid rocket fuel regression rate is thus shown to be describable in a consistent manner in terms of reactive species catalysis of polymer degradation.
Stickler, D. B.↗
Detection techniques for tenuous planetary atmospheres
The research for the development of new types of detectors for analysis of planetary atmospheres is summarized. Topics discussed include: corona discharge humidity detector, surface catalysis and exo-electron emission, and analysis of soil samples by means of exo-electron emission. A report on the exo-electron emission during heterogeneous catalysis is included.
Hoenig, S. A.↗
Interstellar molecules - Origin by catalytic reactions on grain surfaces
To determine the compound distribution formed by surface catalysis, mixtures of CO, D2, and ND2 were heated with nickel-iron or montmorillonite clay catalysts for 49-214 hours at 250 to 300 C. Compounds identified include most of the known polyatomic interstellar molecules, as well as homologous series of acetylenes, dienes, alcohols, aldehydes, ketones, ethers, esters, nitriles, amines, etc., and cyclic compounds such as furans and pyrroles. These homologous series are uniquely characteristic of surface catalysis. A search for the heavier members of these series, predicted to occur at 1/10th to 1/1,000th the abundance of the lightest members, thus comprises a crucial test of this mechanism.
Anders, E.↗
On the origin of molecular 'handedness' in living systems
Elementary particle effects (beta-decay) provide only a weakly handed radiation in the biologically effective energy ranges. Global magnetic effects coupled to sunlight are randomized by paleomagnetic reversals. A persistent terrestrial handed bias at possible local biopoetic sites offers a more promising explanation for the origin of the 'handedness' of the molecules found among living systems on earth. Magnetite in lava flows maintains a handed bias for surface catalysis through many magnetic reversals. Indirect evidence for the hypothesis that magnetite contaminated with sulfur is a possible biopoetic site (Granick, 1957) has been provided by the molecular structure of ferredoxin - a single strand of the 14 primordial amino acids wrapped around an FeS core. Lava flows have been suggested as biopoetic sites by Fox (1964), since their temperature and chemical composition might allow for the rapid synthesis of prebiotic compounds at the surface of the primitive earth. The additional fact that magetite in lava flows also provides a persistent handed site for surface catalysis offers a further argument for the experimental investigation of this specific biopoetic environment.
Noyes, H. P.↗
Cooperation of catalysts and templates
In order to understand how self-reproducing molecules could have originated on the primitive Earth or extraterrestrial bodies, it would be useful to find laboratory models of simple molecules which are able to carry out processes of catalysis and templating. Furthermore, it may be anticipated that systems in which several components are acting cooperatively to catalyze each other's synthesis will have different behavior with respect to natural selection than those of purely replicating systems. As the major focus of this work, laboratory models are devised to study the influence of short peptide catalysts on template reactions which produce oligonucleotides or additional peptides. Such catalysts could have been the earliest protoenzymes of selective advantage produced by replicating oligonucleotides. Since this is a complex problem, simpler systems are also studied which embody only one aspect at a time, such as peptide formation with and without a template, peptide catalysis of nontemplated peptide synthesis, and model reactions for replication of the type pioneered by Orgel.
White, D. H.↗
Role of minerals in the thermal alteration of organic matter. I - Generation of gases and condensates under dry condition
Pyrolysis experiments conducted at 200 and 300 C on kerogen and bitumen from the Monterey formation and on the Green River Formation kerogen with montmorillonite, illite, and calcite added are described. The pyrolysis products are identified and gas and condensate analyses are performed. A catalytic effect is detected in the pyrolysis of kerogen with montmorillonite; however, illite and calcite display no catalytic activity. The increased production of C1-C6 hydrocarbons and the dominance of branched hydrocarbons in the C4-C6 range reveals a catalytic influence. It is observed that the catalysis of montmorillonite is greater during bitumen pyrolysis than for kerogen, and catalysis with minerals affects the production of CO2. It is concluded that a mineral matrix is important in determining the type and amount of gases and condensates forming from organic matter under thermal stress.
Tannenbaum, E.↗
High repetition rate sealed CO2 TEA lasers using heterogeneous catalysts
The significant operational advantages offered by CO2 lasers, operating in the 10.6 micron region of the spectrum, over current solid state lasers, emitting in the near IR region, have prompted increased interest in the development of compact, reliable, rugged CO2 laser sources. Perhaps the most critical aspect associated with achieving a laser compatible with military use is the development of lasers which require no gas replenishment. Sealed, single shot, CO2 TEA lasers have been available for a number of years. Stark et al were first to demonstrate reliable sealed operation in single shot CO2 TEA lasers in 1975 using gas catalysis. GEC Avionics reported the compact, environmentally qualified, MKIII CO2 TEA laser with a pulse life of greater than 10 to the 6th power pulses in 1980. A sealed laser lifetime of greater than 10 to the 6th power pulses is acceptable for single shot cases, such as direct detection rangefinders for tank laser sights. However, in many other applications, such as tracking of fast moving targets, it is essential that a repetition rate of typically 30Hz to 100Hz is employed. In such cases, a pulse lifetime of 10 to the 6th power pulses is no longer sufficient and a minimum pulse lifetime 10 to the 7th power pulses is essential to ensure a useful service life. In 1983 Stark el al described a sealed, 100Hz CO2 TEA laser, with a life of greater than 2.6 x 10 to the 6th power, which employed heterogeneous catalysis. Following this pioneering work, GEC Avionics has been engaged in the development of sealed high repetition rate lasers with a pulse lifetime of 20 million pulses.
Price, H. T.↗
Cosmic strings and baryon decay
The current literature is reviewed on baryon decay catalysis by cosmic string. A summary is presented of the main arguments for decay catalysis.
Gregory, Ruth↗
Origin of fatty acid synthesis - Thermodynamics and kinetics of reaction pathways
The primitiveness of contemporary fatty acid biosynthesis was evaluated by using the thermodynamics and kinetics of its component reactions to estimate the extent of its dependence on powerful and selective catalysis by enzymes. Since this analysis indicated that the modern pathway is not primitive because it requires sophisticated enzymatic catalysis, an alternative pathway of primitive fatty acid synthesis is proposed that uses glycolaldehyde as a substrate. In contrast to the modern pathway, this primitive pathway is not dependent on an exogenous source of phosphoanhydride energy. Furthermore, the chemical spontaneity of its reactions suggests that it could have been readily catalyzed by the rudimentary biocatalysts available at an early stage in the origin of life.
Weber, Arthur L.↗