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Results for “Catalysis and mechanisms of reactions”

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All sourcesNASA NTRSDOE OSTI
NASA NTRS2017

Development of a Detailed Surface Chemistry Framework in DSMC

Many of the current direct simulation Monte Carlo (DSMC) codes still employ only simple surface catalysis models. These include only basic mechanisms such as dissociation, recombination, and exchange reactions, without any provision for adsorption and finite rate kinetics. Incorporating finite rate chemistry at the surface is increasingly becoming a necessity for various applications such as high speed re-entry flows over thermal protection systems (TPS), micro-electro-mechanical systems (MEMS), surface catalysis, etc. In the recent years, relatively few works have examined finite-rate surface reaction modeling using the DSMC method.In this work, a generalized finite-rate surface chemistry framework incorporating a comprehensive list of reaction mechanisms is developed and implemented into the DSMC solver SPARTA. The various mechanisms include adsorption, desorption, Langmuir-Hinshelwood (LH), Eley-Rideal (ER), Collision Induced (CI), condensation, sublimation, etc. The approach is to stochastically model the various competing reactions occurring on a set of active sites. Both gas-surface (e.g., ER, CI) and pure-surface (e.g., LH, desorption) reaction mechanisms are incorporated. The reaction mechanisms could also be catalytic or surface altering based on the participation of the bulk-phase species (e.g., bulk carbon atoms). Marschall and MacLean developed a general formulation in which multiple phases and surface sites are used and we adopt a similar convention in the current work. Microscopic parameters of reaction probabilities (for gas-surface reactions) and frequencies (for pure-surface reactions) that are require for DSMC are computed from the surface properties and macroscopic parameters such as rate constants, sticking coefficients, etc. The energy and angular distributions of the products are decided based on the reaction type and input parameters. Thus, the user has the capability to model various surface reactions via user-specified reaction rate constants, surface properties and parameters.

Gas↗
NASA NTRS1995

Molecular dynamics studies of simple membrane-water interfaces: Structure and functions in the beginnings of cellular life

Molecular dynamics computer simulations of the structure and functions of a simple membrane are performed in order to examine whether membranes provide an environment capable of promoting protobiological evolution. Our model membrane is composed of glycerol 1-monooleate. It is found that the bilayer surface fluctuates in time and space, occasionally creating thinning defects in the membrane. These defects are essential for passive transport of simple ions across membranes because they reduce the Born barrier to this process by approximately 40%. Negative ions are transferred across the bilayer more readily than positive ions due to favorable interactions with the electric field at the membrane-water interface. Passive transport of neutral molecules is, in general, more complex than predicted by the solubility-diffusion model. In particular, molecules which exhibit sufficient hydrophilicity and lipophilicity concentrate near membrane surfaces and experience 'interfacial resistance' to transport. The membrane-water interface forms an environment suitable for heterogeneous catalysis. Several possible mechanisms leading to an increase of reaction rates at the interface are discussed. We conclude that vesicles have many properties that make them very good candidates for earliest protocells. Some potentially fruitful directions of experimental and theoretical research on this subject are proposed.

Pohorille, Andrew↗
NASA NTRS1991

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↗
NASA NTRS1984

Mechanism of the atmospheric oxidation of sulfur dioxide - Catalysis by hydroxyl radicals

A flash photolysis/resonance fluorescence technique was used to investigate the decay of OH due to the reaction OH + SO2 (+M) to HOSO2 (+M). In the presence of small amounts of NO (10 to the 14th per cu cm), the decays deviated from the normal semilogarithmic linearity due to reformation of OH. On the basis of computer simulations of the decay curves, it is suggested that the reactions HOSO2 + O2 to HO2 + SO3 (k3), and HO2 + HO to OH + NO2 are the likely subsequent steps in SO2 oxidation. The upper limit for the binding energy of HOSO2 relative to OH + SO2 is estimated to be 32 kcal/mol. The atmospheric implications of a catalytic oxidation mechanism are briefly discussed.

Margitan, J. J.↗
NASA NTRS1982

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.↗
NASA NTRS1982

Catalytic processes in the atmospheres of earth and Venus

Photochemical processes in planetary atmospheres are strongly influenced by catalytic effects of minor constituents. Catalytic cycles in the atmospheres of Earth and Venus are closely related. For example, chlorine oxides (ClOx) act as catalysts in the two atmospheres. On earth, they serve to convert odd oxygen (atomic oxygen and ozone) to molecular oxygen. On Venus they have a similar effect, but in addition they accelerate the reactions of atomic and molecular oxygen with carbon monoxide. The latter process occurs by a unique combination of ClOx catalysis and sulful dioxide photosensitization. The mechanism provides an explanation for the very low extent of carbon dioxide decomposition by sunlight in the Venus atmosphere.

Demore, W. B.↗
NASA NTRS2022

CryoEM Structures of the Nitrogenase Complex During Catalytic Turnover

The enzyme nitrogenase couples adenosine triphosphate (ATP) hydrolysis to the multi-electron reduction of atmospheric dinitrogen into ammonia. Despite extensive research, the mechanistic details of ATP-dependent energy transduction and dinitrogen reduction by nitrogenase are not well understood, requiring new strategies to monitor its structural dynamics during catalytic action. Here we report the cryogenic electron microscopic interrogation of the nitrogenase complex under enzymatic turnover conditions, which has enabled the structural characterization of the nitrogenase reaction intermediates at high resolution for the first time. Our structures show that asymmetry governs all aspects of nitrogenase mechanism including ATP hydrolysis, protein-protein interactions, and catalysis. Furthermore, they reveal several previously unobserved, mechanistically relevant conformational changes near the catalytic iron-molybdenum cofactor that are correlated with the nucleotide-hydrolysis state of the enzyme.

Hannah L. Rutledge↗
NASA NTRS2001

Catalysis in the 3rd Dimension: How Organic Molecules May be Formed

Catalysis is often little more than a word to phenomenologically describe the fact that a reaction follows a pat1 that leads to products of an unexpected kind or of unexpected yield. Low activation energy barriers for intermediates are recognized as the most likely cause why a system deviates from the thermodynamic pull towards minimizing its free energy and ends up in a metastable state. Seldom is the mechanism known. This i: particularly true for heterogeneous catalysis under hydrothermal conditions with minerals as catalysts. It is commonly assumed that catalytic action takes place across solid-fluid interfaces and that, on the atomic level, interfaces are just 2-dimensional contacts. This makes it difficult to understand, for instance, the assembly of long-chain carboxylic (fatty) acids. 3y studying single crystals that grew from a melt in the presence of H2O and CO2, we can show: (1) that numerals take up the fluid components into solid solution, (2) that some-thing happens converting them to -educedH and C, (3) that C atoms segregate into dislocations and tie C-C bonds. The products are medium-to-long chain Cn protomolecules, with some C-H attached, pre-assembled in the dislocations. Upon solvent extraction, these proto-molecules turn into carboxylic and dicarboxylic acids. This observation suggests that, in a very elementary step, catalysis under hydrothermal conditions leading to fatty acids involves the pre-assembly of Cn entities in the interface that is not 2-D but extends into the 3rd dimension, with dislocations as synthesis sites.

Freund, Friedemann↗
NASA NTRS2014

Evaluating the Adsorptive Capabilites of Chemsorb 1000 and Chemsorb 1425

The removal of trace contaminants from spacecraft cabin air is necessary for crew health and comfort during long duration space exploration missions. The air revitalization technologies used in these future exploration missions will evolve from current ISS ISS State-of-Art (SOA) and is being designed and tested by the Advanced Exploration Systems (AES) Program's Atmosphere Resource Recovery and Environmental Monitoring (ARREM) project. The ARREM project is working to mature optimum atmosphere revitalization and environmental monitoring system architectures to enable exploration beyond Lower Earth Orbit (LEO). The Air Revitalization Lab at KSC is one of six NASA field centers participating in the ARREM that specializes in adsorbent and catalyst characterization with simulated spacecraft gas streams using combinations of pressure, O2 partial pressure, CO2 partial pressure, and humidity that are representative of a range of anticipated cabin atmospheric conditions and loads. On board ISS, the Trace Contaminant Control Subassembly (TCCS) provides active control of trace contaminants from the cabin atmosphere utilizing physical adsorption, thermal catalytic oxidation, and chemical adsorption processes. High molecular weight contaminants and ammonia (NH3) are removed a granular activated carbon treated with approx. 10% by weight phosphoric acid (H3PO4) (B-S Type 3032 4×6 mesh), which is expendable and is periodically refurbished. The Type 3032 granular activated carbon bed is no longer commercially available and therefore it is important to characterize the efficiency and capacity of commercially available NH3 sorbents. This paper describes the characterization of two Molecular Products LTD activated carbons: Chemsorb 1000 and Chemsorb 1425. Untreated activated carbons (e.g. Chemsorb 1000) remove contaminants by physisorption, which concentrates the contaminant within the pores of the carbon while letting air to pass through the sorbent4. Low molecular weight or polar gases (e.g. HCl, SO2, formaldehyde, and NH3) are not removed by physisorption and typically require chemisorption for removal. Treated activated carbons (e.g. Chemsorb 1425) are impregnated with a a chemical agent (e.g. phosphoric acid) that reacts with those gases, converting them to solids or salts within the carbon and removes them from the air stream. This process occurs via neutralization or catalysis reactions and adsorption capacity is exhaustedwhen the available impregnated chemicals are consumed. Moisture affects removal performance since adsorption sites within the pores are filled with water. The performance of impregnated carbons may be enhanced by moisture content because the mechanisms of contaminant removal are chemical reactions that occur in reagents contained within the pores. The adsorptive capacity data (mol/kg) of Chemsorb 1000 and 1425 for gas mixtures (ethanol, acetone, toluene, acetaldehyde, dichloromethane, and xylene) was measured with 40% relative humidity at 23 deg C air temperature. The adsorptive capacity data (mol/kg) of Chemsorb 1425 was measured using NH3 gas streams.

adsorptive capacities↗
NASA NTRS1971

The effect of imidazole, cyanamide, and polyornithine on the condensation of nucleotides in aqueous systems.

Development of two models for the condensation of nucleotides under possibly prebiotic conditions. In the first of these models this type of reaction is promoted by the presence of imidazole and substituted imidazole compounds. The second model involves the condensation of mononucleotides with cyanamide in the presence and absence of a prototemplate such as polyornithine. A tentative mechanism for the role of imidazole catalysis in phosphodiester bond formation between adjacent TMP molecules is suggested.

Ibanez, J.↗
NASA NTRS1997

The Effect of Diffusional Transport and Surface Catalysis on the Aerothermodynamic Heating for Martian Atmospheric Entry

For the reentry heating of 70-degree blunt sphere-cones entering Mars at velocities in excess of 6 km/sec, a study was performed to determine the magnitude of both convective and catalytic heating on the cone forebody. Case studies of the peak heating conditions for the current NASA Mars Pathfinder entry probe, as well as the peak heating conditions of the proposed NASA Mars 2001 aerobraking orbiter mission were performed. Since the actual behavior of the chemical recombination of Mars atmosphere hypersonic shock layer species on heat shield materials is not known, and no experimental studies of any consequence have been done to determine surface reaction rates for the CO2 system, a parametric analysis of various reaction schemes and surface catalytic mechanistic models was performed. In many cases the actual Mars entry probe will have a heat shield composed of an ablative material which can either partially or completely preclude the existence of catalytic surface recombination phenomena. The extent of this blockage effect has not been examined at this time and is not considered in this effort. Instead only non-ablative computations are performed to separately evaluate the full extent of the surface catalysis and related diffusional phenomena. Parametric studies include peak heating point comparisons of non-catalytic, partially catalytic and fully catalytic total surface heat transfer for three difference surface recombination catalytic mechanisms (with and without simultaneous CO + O and O + O recombination) as well as with different species diffusion models. Diffusion model studies include constant Schmidt number (equal diffusivities) and the bifurcation, approximate multi-component diffusion model. Since the gas phase reaction kinetics for the Mars CO2 based atmosphere have also not been validated, the effect of two different (fast and slow) sets of gas kinetics on heat transfer is presented.

Henline, William D.↗
NASA NTRS1995

Self-Incorporation of Coenzymes by Ribozymes

RNA molecules that are assembled from the four standard nucleotides contain a limited number of chemical functional groups, a characteristic that is generally thought to restrict the potential for catalysis by ribozymes. Although polypeptides carry a wider range of functional groups, many contemporary protein-based enzymes employ coenzymes to augment their capabilities. The coenzymes possess additional chemical moieties that can participate directly in catalysis and thereby enhance catalytic function. In this work, we demonstrate a mechanism by which ribozymes can supplement their limited repertoire of functional groups through RNAcatalyzed incorporation of various coenzymes and coenzyme analogues. The group I ribozyme of Tetrahymena thermophila normally mediates a phosphoester transfer reaction that results in the covalent attachment of guanosine to the ribozyme. Here, a shortened version of the ribozyme is shown to catalyze the self-incorporation of coenzymes and coenzyme analogues, such as NAD+ and dephosphorylated CoA-SH. Similar ribozyme activities may have played an important role in the "RNA world," when RNA enzymes are thought to have maintained a complex metabolism in the absence of proteins and would have benefited from the inclusion of additional functional groups.

Breaker, Ronald R.↗
NASA NTRS1991

Nucleotides as nucleophiles: reactions of nucleotides with phosphoimidazolide activated guanosine

An earlier study of the reaction of phosphoimidazolide activated nucleosides (ImpN) in aqueous phosphate buffers indicated two modes of reaction of the phosphate monoanion and dianion. The first mode is catalysis of the hydrolysis of the P-N bond in ImpN's which leads to imidazole and nucleoside 5'-monophosphate. The second represents a nucleophilic substitution of the imidazole to yield the nucleoside 5'-diphosphate. This earlier study thus served as a model for the reaction of ImpN with nucleoside monophosphates (pN) because the latter can be regarded as phosphate derivatives. In the present study we investigated the reaction of guanosine 5'-phosphate-2-methylimidazolide, 2-MeImpG, in the presence of pN (N = guanosine, adenosine and uridine) in the range 6.9 less than or equal to pH less than or equal to 7.7. We observed that pN's do act as nucleophiles to form NppG, and as general base to enhance the hydrolysis of the P-N bond in 2-MeImpG, i.e. pN show the same behavior as inorganic phosphate. The kinetic analysis yields the following rate constants for the dianion pN2-: knpN = 0.17 +/- 0.02 M-1 h-1 for nucleophilic attack and khpN = 0.11 +/- 0.07 M-1 h-1 for general base catalysis of the hydrolysis. These rate constants which are independent of the nucleobase compare with kp.2 = 0.415 M-1 h-1 and khp2. = 0.217 M-1 h-1 for the reactions of HPO4(2-). In addition, this study shows that under conditions where pN presumably form stacks, the reaction mechanism remains unchanged although in quantitative terms stacked pN are somewhat less reactive. Attack by the 2'-OH and 3'-OH groups of the ribose moiety in amounts greater than or equal to 1% is not observed; this is attributed to the large difference in nucleophilicity in the neutral pH range between the phosphate group and the ribose hydroxyls. This nucleophilicity rank is not altered by stacking.

NASA Discipline Exobiology↗
NASA NTRS1996

Kinetic and mechanistic analysis of nonenzymatic, template-directed oligoribonucleotide ligation

The role of divalent cations in the mechanism of pyrophosphate-activated, template-directed oligoribonucleotide ligation has been investigated. The dependence of the reaction rate on Mg2+ concentration suggests a kinetic scheme in which a Mg2+ ion must bind before ligation can proceed. Mn2+, Ca2+, Sr2+, and Ba2+ can also catalyze the reaction. Although Pb2+ and Zn2+ do not catalyze the reaction in the absence of other divalent ions, they significantly modulate the reaction rate when added in the presence of Mg2+, with Pb2+ stimulating the reaction (up to 65-fold) and Zn2+ inhibiting the reaction. The logarithm of the ligation rate increases linearly, with slope of 0.95, as a function of pH, indicating that the reaction involves a single critical deprotonation step. The ligation rates observed with the different divalent metal ion catalysts (Mn2+ > Mg2+ > Ca2+ > Sr2+ = Ba2+) vary inversely with the pKa values of their bound water molecules. The pH profile and these relative ligation rates suggest a mechanism in which a metal-bound hydroxide ion located near the ligation junction promotes catalysis, most likely by deprotonation of the hydroxl nucleophile. The effects of changing either the leaving group or the attacking hydroxyl, together with the large delta S(++) value for oligonucleotide ligation (about -20 eu), are consistent with an associative transition state.

Non-NASA Center↗
NASA NTRS2024

Two mechanisms for the spontaneous emergence, execution, and reprogramming of chemical logic circuits

A key question in origin-of-life research is how primitive life or life-like systems obtained reusable and reprogrammable machinery of processing information to respond to various environmental and internal stimuli. One strategy to approach this question is to view living systems as universal chemical computers. This approach focuses upon uncovering how reusable and reprogrammable chemical NOT, AND, and OR logic gates could appear under prebiotically possible scenarios where simple chemicals and second- or lower-order reactions are more frequent than macromolecules and higher-order reactions. In this article, we theoretically model two generic mechanisms of forming Boolean gates based on geochemically plausible reaction systems that could have preceded complex biopolymers. The mechanisms exploit simple bistable autocatalytic systems to encode binary variables and use heterogeneous dilution rates to differentially activate or deactivate autocatalysis in different reactors. We found that NOT, AND, and OR gates, as well as more complex logic circuits, can spontaneously arise from connected, well-mixed flow reactors based on (i) catalysis by a heterodimer between mutually inhibitory autocatalysts or (ii) selectively permeable tunnels connecting reactors. Our results suggest that simple machinery can support the prebiotic emergence of complex chemical logic circuits and provide new guides for experimentally actualizing chemical computation.

Zhen Peng↗
NASA NTRS1984

The prebiotic chemistry of nucleotides

Diminosuccinonitrile (DISN), formed by the oxidation of diaminomaleonitrile, has been investigated as a potential prebiotic phosphorylating agent. DISN affects the cyclization of 3'-adenosine monophosphate to adenosine 2',3'-cyclic phosphate in up to 39 percent yield. The mechanism of this reaction was investigated. The DISN-mediated phosphorylation of uridine to uridine monophosphate does not proceed efficiencly in aqueous solution. The reaction of DISN with uridine-5'-phosphate and uridine results in the formation of 2,2'-anhydronucleotides and 2,2'-anhydronucleosides respectively, and other reaction products resulting from an initial reaction at the 2'- and 3'-hydroxyl groups. The clay mineral catalysis of the cyclization of adenosine-3'-phosphate was investigated using homoionic montmorillonites.

Ferris, J. P.↗
NASA NTRS1981

Condensation of activated diguanylates on a Poly/C/ template

The metal-ion catalysis of the oligomerization of activated diguanylate isomers on a polycytidylic acid template is studied in an investigation of possible early prebiotic polynucleotide replication mechanisms. The 5'-imidazolides of diguanylates linked 2' to 5' or 3' to 5' were reacted with polyC in a 1-methylimidazole or a 2,6-lutidine buffer in the presence of a Zn(+2) or a Pb(+2) catalyst, and reaction products were determined by paper chromatography, paper electrophoresis and liquid chromatography. In the lutidine buffer, the presence of both the Zn(+2) catalyst and the polyC template is found to result in the production of 3'-5' linked oligomers with up to 10 diguanylate units, and from diguanylates in the presence of the monomer. In the reactions conducted in the 1-methylimidazole buffer, the addition of Pb(+2) is found to lead to less marked increases in oligomerization in the presence of template, with approximately equal proportions of 2'-5' and 3'-5' oligomers formed from the 2'-5' substrate and mainly 3'-5' bonds from the 3'-5' linked dimer.

Lohrmann, R.↗
NASA NTRS1997

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↗