Early Nitrogenase Ancestors Encompassed Novel Active Site Diversity
Explore the source record for details and available documents.
Sarah L Schwartz↗
SEARCH · Engineering Papers
Results for “active sites”
Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.
Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.
Computational Study of Oxidative Etch Pitting in FiberForm and the Effect on Its Material Properties
Erosion of carbon due to oxidation does not occur uniformly but through the formation of localized etch pits because of active surface sites. These active sites are formed due to the presence of atomic defects on the carbon surface, and have much higher reactivity compared to average non-defective sites. Thus, these active sites are first to react during ablation, resulting in their removal. This causes all the neighboring atoms to be defective and increase their reactivity, thus leading to the localized carbon removal around these “active” sites. In this manner, these highly reactive defective sites serve as nucleation sites for the formation and growth of etch pits with potentially detrimental effects on the structural integrity. In order to understand the influence of these etch pits on the material properties of carbon fiber microstructures, we have developed a new capability within direct simulation Monte Carlo (DSMC) to capture the etch pit formation process. This capability is developed within the DSMC code SPARTA (Stochastic PArallel Rarefied-gas Time-accurate Analyzer) and can model the material removal in presence of active sites leading to the formation of etch pits. The focus of the current work will be to study the effect of etch pits on the material properties of FiberForm, a commonly used base material within many thermal protection system materials (TPS). The microstructure of virgin FiberForm obtained directly from X-ray microtomography experiments is used within SPARTA to obtain the ablated geometries with etch pits. These pitted microstructures are then imported within the Porous Microstructure Analysis (PuMA) software and various material properties such as elasticity, thermal conductivity, and permeability are computed. The variation of these properties as a result of the complex evolution of the surface topology due to etch pit formation is studied and analyzed. Furthermore, the effect of pitting is compared to the case of shrinking fibers, which has been the standard for modelling ablation of carbon structures; and significant differences are observed. Thus, such a physically realistic modeling of material removal through the formation of etch pits will be helpful in predicting the degradation of carbon-based TPS more accurately during oxidation; as well as other mechanisms such as spallation, which involves the removal of chunks of material into the flow due to etch pit growth. This will ultimately improve our understanding of the failure modes in these materials due to ablation.
Carbon Ablators↗
Computational Study of Oxidative Etch Pitting in FiberForm and the Effect on Its Material Properties
Erosion of carbon due to oxidation does not occur uniformly but through the formation of localized etch pits because of active surface sites. These active sites are formed due to the presence of atomic defects on the carbon surface, and have much higher reactivity compared to average non-defective sites. Thus, these active sites are first to react during ablation, resulting in their removal. This causes all the neighboring atoms to be defective and increase their reactivity, thus leading to the localized carbon removal around these “active” sites. In this manner, these highly reactive defective sites serve as nucleation sites for the formation and growth of etch pits with potentially detrimental effects on the structural integrity. In order to understand the influence of these etch pits on the material properties of carbon fiber microstructures, we have developed a new capability within direct simulation Monte Carlo (DSMC) to capture the etch pit formation process. This capability is developed within the DSMC code SPARTA (Stochastic PArallel Rarefied-gas Time-accurate Analyzer) and can model the material removal in presence of active sites leading to the formation of etch pits. The focus of the current work will be to study the effect of etch pits on the material properties of FiberForm, a commonly used base material within many thermal protection system materials (TPS). The microstructure of virgin FiberForm obtained directly from X-ray microtomography experiments is used within SPARTA to obtain the ablated geometries with etch pits. These pitted microstructures are then imported within the Porous Microstructure Analysis (PuMA) software and various material properties such as elasticity, thermal conductivity, and permeability are computed. The variation of these properties as a result of the complex evolution of the surface topology due to etch pit formation is studied and analyzed. Furthermore, the effect of pitting is compared to the case of shrinking fibers, which has been the standard for modelling ablation of carbon structures; and significant differences are observed. Thus, such a physically realistic modeling of material removal through the formation of etch pits will be helpful in predicting the degradation of carbon-based TPS more accurately during oxidation; as well as other mechanisms such as spallation, which involves the removal of chunks of material into the flow due to etch pit growth. This will ultimately improve our understanding of the failure modes in these materials due to ablation.
Carbon Ablators↗
Simulation of Oxidative Etch Pit Formation and Growth on FiberForm
Erosion of carbon surfaces due to oxidation does not occur uniformly but through the formation of localized etch pits because of active surface sites. These active sites are formed due to the presence of atomic defects on the carbon surface and have much higher reactivity compared to average non-defective sites. Thus, these active sites are the first to react during ablation, resulting in their removal. This causes all the neighboring atoms to be defective, and increasing their reactivity, thus leading to localized carbon removal around these “active” sites. In this manner, these highly reactive defects serve as nucleation sites for the formation and growth of etch pits, with detrimental effects on the structural integrity. In order to understand the influence of these etch pits on the material properties of carbon fiber microstructures, we have developed a new capability within direct simulation Monte Carlo (DSMC) to capture the etch pit formation process. This capability is developed within the DSMC code SPARTA (Stochastic PArallel Rarefied-gas Time-accurate Analyzer) and can model the material removal in the presence of active sites leading to the formation of etch pits. The focus of the current work will be to study the effect of etch pits on the material properties of FiberForm, the precursor substrate of the PICA Thermal Protection System (TPS) material. The microstructure of virgin FiberForm obtained directly from X-ray microtomography scans is used within SPARTA to obtain the ablated geometries with etch pits. These pitted microstructures are then imported into the Porous Microstructure Analysis (PuMA) software and various material properties such as thermal conductivity, elasticity, and permeability are computed. The variation of these properties because of the complex evolution of the surface topology due to the formation of etch pits is studied and analyzed. Furthermore, the effect of pitting is compared to the case of uniform radial shrinking of fibers, which has been the standard for modelling ablation of carbon structures, and significant differences are observed. Thus, a physically realistic model of material removal through the formation of etch pits will be helpful in predicting the degradation of carbon-based TPS more accurately during oxidation; as well as other mechanisms such as spallation, which involves the removal of chunks of material into the flow due to the growth of etch pits. This will ultimately improve our understanding of the failure modes in these materials due to ablation.
DSMC↗
Simulation of Oxidative Etch Pit Formation and Growth on FiberForm
Erosion of carbon surfaces due to oxidation does not occur uniformly but through the formation of localized etch pits because of active surface sites. These active sites are formed due to the presence of atomic defects on the carbon surface and have much higher reactivity compared to average non-defective sites. Thus, these active sites are the first to react during ablation, resulting in their removal. This causes all the neighboring atoms to be defective, and increasing their reactivity, thus leading to localized carbon removal around these “active” sites. In this manner, these highly reactive defects serve as nucleation sites for the formation and growth of etch pits, with detrimental effects on the structural integrity. In order to understand the influence of these etch pits on the material properties of carbon fiber microstructures, we have developed a new capability within direct simulation Monte Carlo (DSMC) to capture the etch pit formation process. This capability is developed within the DSMC code SPARTA (Stochastic PArallel Rarefied-gas Time-accurate Analyzer) and can model the material removal in the presence of active sites leading to the formation of etch pits. The focus of the current work will be to study the effect of etch pits on the material properties of FiberForm, the precursor substrate of the PICA Thermal Protection System (TPS) material. The microstructure of virgin FiberForm obtained directly from X-ray microtomography scans is used within SPARTA to obtain the ablated geometries with etch pits. These pitted microstructures are then imported into the Porous Microstructure Analysis (PuMA) software and various material properties such as thermal conductivity, elasticity, and permeability are computed. The variation of these properties because of the complex evolution of the surface topology due to the formation of etch pits is studied and analyzed. Furthermore, the effect of pitting is compared to the case of uniform radial shrinking of fibers, which has been the standard for modelling ablation of carbon structures, and significant differences are observed. Thus, a physically realistic model of material removal through the formation of etch pits will be helpful in predicting the degradation of carbon-based TPS more accurately during oxidation; as well as other mechanisms such as spallation, which involves the removal of chunks of material into the flow due to the growth of etch pits. This will ultimately improve our understanding of the failure modes in these materials due to ablation.
DSMC↗
Automated protein crystal growth facility
A customer for the protein crystal growth facility fills the specially designed chamber with the correct solutions, fills the syringes with their quenching solutions, and submits the data needed for the proper growth of their crystal. To make sure that the chambers and syringes are filled correctly, a NASA representative may assist the customer. The data needed is the approximate growth time, the growth temperature, and the desired crystal size, but this data can be changed anytime from the ground, if needed. The chambers are gathered and placed into numbered slots in special drawers. Then, data is entered into a computer for each of the chambers. Technicians map out when each chamber's growth should be activated so that all of the chambers have enough time to grow. All of this data is up-linked to the space station when the previous growth session is over. Anti-vibrational containers need to be constructed for the high forces encountered during the lift off and the landing of the space shuttle, and though our team has not designed these containers, we do not feel that there is any reason why a suitable one could not be made. When the shuttle reaches the space station, an astronaut removes a drawer of quenched chambers from the growth facility and inserts a drawer of new chambers. All twelve of the drawers can be replaced in this fashion. The optical disks can also be removed this way. The old drawers are stored for the trip back to earth. Once inside the growth facility, a chamber is removed by the robot and placed in one of 144 active sites at a time previously picked by a technician. Growth begins when the chamber is inserted into an active site. Then, the sensing system starts to determine the size of the protein crystal. All during the crystal's growth, the customer can view the crystal and read all of the crystal's data, such as growth rate and crystal size. When the sensing system determines that the crystal has reached the predetermined size, the robot is told to pick up a syringe filled with the correct quenchant solution and inject it into the chamber to stop the crystal growth. The chamber is then removed from the active site and placed into its original storage slot. Another chamber is then placed into the active site and the process is repeated in all of the active sites until all of the chambers have complted their growth. After ninety days (the scheduled time between shuttle visits), the crystal growth is completed, and the old drawers are replaced with new ones. Once the customer extracts the crystals, the chambers are retrieved for future customers.
Donald, Stacey↗
Cryo-Trapping the Distorted Octahedral Reaction Intermediate of Manganese Superoxide Dismutase
Superoxide dismutase protects organisms from potentially damaging oxygen radicals by catalyzing the disproportion of superoxide to oxygen and hydrogen peroxide. We report the use of cryogenic temperatures to kinetically trap the 6th ligand bound to the active site of manganese superoxide dismutase. Using cryocrystallography and synchrotron radiation, we describe at 1.55A resolution the six-coordinate, distorted octahedral geometry assumed by the active site during catalysis and compare it to the room temperature, five-coordinate trigonal-bipyramidal active site. Gateway residues Tyr34, His30 and a tightly bound water molecule are implicated in closing off the active site and blocking the escape route of superoxide during dismutation.
Borgstahl, Gloria↗
Cryo-Trapping the Distorted Octahedral Reaction Intermediate of Manganese Superoxide Dismutase
Superoxide dismutase protects organisms from potentially damaging oxygen radicals by catalyzing the disproportion of superoxide to oxygen and hydrogen peroxide. We report the use of cryogenic temperatures to kinetically trap the 6th ligand bound to the active site of manganese superoxide dismutase. Using cryocrystallography and synchrotron radiation, we describe at 1.55A resolution the six-coordinate, distorted octahedral geometry assumed by the active site during catalysis and compare it to the room temperature, five-coordinate trigonal-bipyramidal active site. Gateway residues Tyr34, His30 and a tightly bound water molecule are implicated in closing off the active site and blocking the escape route of superoxide during dismutation.
Borgstahl, Gloria↗
Preparation and Characterization of Fluorescent Derivatives of Chicken Egg White Lysozyme
Fluorescence is one of the most versatile and powerful tools for the study of macromolecules. While most proteins are intrinsically fluorescent, working at crystallization concentrations require the use of covalently prepared derivatives added as tracers. This approach requires derivatives that do not markedly affect the crystal packing. We have prepared a number of fluorescent derivatives of chicken egg white lysozyme with probes bound to one of two different sites on the protein molecule. Lucifer yellow, cascade blue, and 5-(2-aminoethyl)aminonapthalene-l-sulfonic acid (EDANS) have been attached to the side chain carboxyl of asp101 using a carbodiimide coupling procedure. asp101 lies within the active site cleft, and it is believed that the probes are at least partially "buried" within that cleft. Lucifer yellow and MANS probes with iodoacetamide reactive groups have been bound to hisl5, located on the "back side" of the molecule relative to the active site. The fluorescently labeled protein is readily purified from the starting material by cation exchange chromatography. All the derivatives fluoresce in both the solution and the crystalline states. Fluorescence characterization has focused on determining the bound probe quantum yields, lifetimes, absorption and emission spectra, and quenching by added solutes in comparison to the free probe. No appreciable changes are found in the lifetimes of any of the probes except for cascade blue, where Tau(sub free) = 3.52 ns vrs Tau(sub bound) = 2.8 ns. Spectral shifts are found in most cases. Particularly strong quenching upon binding is found in the case of the cascade blue derivative, likely due to probe interactions with the active site cleft. While none of the asp101 bound probes are well quenched by commonly employed solutes, such as potassium and sodium iodide, acrylamide, primuline, the chloride salts of manganese, cesium, and cobalt, trifluoroacetamide, trichloroethanol, and thallium iodide, in those cases where quenching is observed the bound probe is less efficiently quenched relative to the free probe. This indicates that the bound probes are less accessible to the bulk solution, an expected finding for attachment within the active site cleft. Attempts have been made to bind other molecules to these sites, with varying success. Interestingly, all three probes contain one or more sulfonate ((Ar-S03)-) groups. We have not been successful in binding analogous probes without sulfate groups such as pyrene, or with derivatized sulfonate groups such as dansyl type probes, analogous to MANS but where the sulfonate group is derivatized, Ar-S02-N2C2H7. None of the probes is rigidly bound to the protein, i.e., they all have a probe motion superimposed on that of the protein.
Sumida, John↗
Method for measuring surface activity of silicon nitride powder
Amorphous, alpha-, and beta-Si3N4 powders were activated by vibration ball milling in purified MeOH, and the surface activity of ground powders was determined by the temperature programmed desorption (TPD) method using NH3 gas. The concentration of active sites with a potential energy equivalent to the peak temperature in the spectrum increased was markedly by ball milling the amorphous Si3N4. The alpha- and beta-Si3N4 also had active sites produced by ball milling. The concentration of active site increased with increased ball milling time. A method for measuring surface activity of ceramic raw materials by TPD is proposed.
Kanno, Y.↗
Computational Investigation of Oxidative Etch Pitting in FiberForm and Its Impact on Material Properties
Oxidation-driven carbon erosion does not occur uniformly but rather through the development of localized etch pits at active surface sites. These active sites form due to atomic defects on the carbon surface, making them significantly more reactive than the surrounding, non-defective areas. As a result, these sites are the first to react during ablation, leading to their removal. This process creates new defects in neighboring atoms, increasing their reactivity and causing localized carbon removal around these active sites. In this way, the highly reactive defective areas serve as nucleation points for the formation and growth of etch pits, which can have adverse effects on structural integrity of FiberForm. To better understand how these etch pits impact the material properties of carbon fiber microstructures, we have developed a new capability within the direct simulation Monte Carlo (DSMC) framework to capture the etch pit formation process. This capability, integrated into the DSMC code SPARTA (Stochastic Parallel Rarefied-gas Time-accurate Analyzer), models material removal in the presence of active sites, leading to the formation of etch pits. The current work focuses on studying the effects of these etch pits on the material properties of FiberForm, a widely used base material in thermal protection systems (TPS). The microstructure of virgin FiberForm, obtained via X-ray microtomography, is imported into SPARTA to generate the ablated geometries with etch pits. These modified microstructures are then analyzed using the Porous Microstructure Analysis (PuMA) software to compute various material properties, including elasticity, thermal conductivity, and permeability. We investigate the variation of these properties due to the complex surface topology changes caused by etch pit formation. Additionally, we compare the effects of pitting with the conventional model of shrinking fibers, traditionally used to simulate the ablation of carbon structures. Significant differences emerge between the two approaches. Consequently, this physically realistic model of material removal through etch pit formation offers improved accuracy in predicting the degradation of carbon-based TPS during oxidation. It also provides insights into other mechanisms, such as spallation, where chunks of material are removed into the flow due to etch pit growth. Ultimately, this model enhances our understanding of failure modes in these materials during ablation.
PuMA↗
Preparation and Preliminary Characterization of Crystallizing Fluorescent Derivatives of Chicken Egg White Lysozyme
Fluorescence is one of the most versatile and powerful tools for the study of macromolecules. While most proteins are intrinsically fluorescent, working at crystallization concentrations require the use of covalently prepared derivatives added as tracers. This approach requires derivatives that do not markedly affect the crystal packing. We have prepared fluorescent derivatives of chicken egg white lysozyme with probes bound to one of two different sites on the protein molecule. Lucifer yellow and 5-(2-aminoethyl)aminonapthalene-1-sulfonic acid (EDANS) have been attached to the side chain carboxyl of Asp(sup 101) using a carbodiimide coupling procedure. Asp(sup 101) lies within the active site cleft, and it is believed that the probes are "buried" within that cleft. Lucifer yellow and MANS probes with iodoacetamide reactive groups have been bound to His(sup 15), located on the "back side" of the molecule relative to the active site. All the derivatives fluoresce in the solution and the crystalline states. Fluorescence characterization has focused on determination of binding effects on the probe quantum yield, lifetime, absorption and emission spectra, and quenching by added solutes. Quenching studies show that, as postulated, the Asp(sup 101)-bound probes are partially sheltered from the bulk solution by their location within the active site cleft. Probes bound to His(sup 15) have quenching constants about equal to those for the free probes, indicating that this site is highly exposed to the bulk solution.
Sumida, John↗
Preparation and Preliminary Characterization of Crystallizing Fluorescent Derivatives of Chicken Egg White Lysozyme
Fluorescence is one of the most versatile and powerful tools for the study of macromolecules. While most proteins are intrinsically fluorescent, working at crystallization concentrations require the use of covalently prepared derivatives added as tracers. This approach requires derivatives that do not markedly affect the crystal packing. We have prepared fluorescent derivatives of chicken egg white lysozyme with probes bound to one of two different sites on the protein molecule. Lucifer yellow and 5-(2-aminoethyl)aminonapthalene-i-sulfonic acid (EDANS) have been attached to the side chain carboxyl of Asp(sup 101) using a carbodiimide coupling procedure. Asp(sup 101) lies within the active site cleft, and it is believed that the probes are 'buried' within that cleft. Lucifer yellow and MANS probes with iodoacetamide reactive five groups have been bound to His(sup 15), located on the 'back side' of the molecule relative to the active site. All the derivatives fluoresce in the solution and the crystalline states. Fluorescence characterization has focused on determination of binding effects on the probe quantum yield, lifetime, absorption and emission spectra, and quenching by added solutes. Quenching studies show that, as postulated, the Asp(sup 101)-bound probes are partially sheltered from the bulk solution by their location within the active site cleft. Probes bound to His(sup 15) have quenching constants about equal to those for the free probes, indicating that this site is highly exposed to the bulk solution.
Sumida, John P.↗
Supporting technology for the development of Controlled Ecological Life Support Systems (CELSS)
To support the development of Controlled Ecological Life Support Systems (CELSS) in the space program, a metabolic simulator has been selected for use in a closed chamber to test functions of the CELSS. This metabolic simulator is a catalytic reactor which oxidizes the methyl acetate to produce carbon dioxide and water vapor. In this project, kinetic studies of catalytic oxidation of methyl acetate were conducted using monolithic and pellet catalysts with 0.5% (by weight) platinum (Pt) on aluminum oxide (Al2O3). The reaction was studied at a pressure of one atmosphere and at temperatures varying from 160 C to 420 C. By-products were identified at the exit of the preheater and reactor. For the kinetic study with the monolithic catalyst, a linear regression method was used to correlate the kinetic data with zero-order, first-order and Langmuir-Hinshelwood models. Results indicate that the first-order model represents the data adequately at low concentrations of methyl acetate. For higher concentrations of methyl acetate, the Langmuir-Hinshelwood model best represents the kinetic data. Both rate constant and adsorption equilibrium constants were estimated from the regression. A Taguchi orthogonal array (L(sub 9)) was used to investigate the effects of temperature, flow rate, and concentration on the catalytic oxidation of methyl acetate. For the monolithic catalyst, temperature exerts the most significant effect, followed by concentration of methyl acetate. For the pellet catalyst, reaction temperature is the most significant factor, followed by gas flow rate and methyl acetate concentration. Concentrations of either carbon dioxide or oxygen were seen to have insignificant effect on the methyl acetate conversion process. Experimental results indicate that the preheater with glass beads can accomplish thermal cracking and catalytic reaction of methyl acetate to produce acetic acid, methanol, methyl formate, and 1-propanol. The concentration of all by-products was measured in ppmv (parts per million by volume). At higher temperatures, greater amounts of these products are produced, as expected. In all cases, methanol was the predominant concentration detected, followed by methyl formate. At temperatures lower than 320 C for the P-type monolithic catalyst, methanol, acetic acid, and acetone were detected, whereas, for the E-type monolithic catalyst, only methanol was detected at 160 C. Both P and E types of the monolithic catalyst were specified with the same substrates (ceramic), washcoat (Al2O3), and promoter (Pt). However, the manufacturing and treatment procedures were quite different. It was therefore concluded that the performance of the E-type monolithic catalyst is superior to that of the P-type for oxidation of methyl acetate. At higher reaction temperatures, e.g., above 420 C, all reactants and byproducts were completely oxidized using these two types of monolithic catalyst to produce carbon dioxide and water vapor. A complex heterogenous catalytic reaction mechanism was proposed to explain the formation of the byproducts (methanol, acetic acid, and methyl formate) as the methyl acetate traveled through the preheater packed with glass beads. The by-product, 1-propanol, may be formed only through a homogeneous reaction, since it is difficult to develop a reasonable sequence of heterogeneous reaction steps to explain its formation. The homogeneous thermal decomposition of methyl acetate to form free radicals was proposed to explain the formation of 1-propanol, and also methanol, in the preheater. A dual-site catalytic reaction mechanism was proposed for the oxidation of methyl acetate over Pt/Al2O3 monolithic catalyst. The dual-site mechanism describes the chemisorption of oxygen molecules as well as a physical adsorption of methyl acetate on the active sites. On the active sites, methyl acetate is oxidized rapidly to form carbon dioxide and water vapor. A rate equation derived from this mechanism gives the Langmuir-Hinshelwood rate formula which has been observed from the experimental data obtained in this project for high methyl acetate concentration (greater than 1000 ppmv) over a monolithic catalyst. If the oxygen concentration is very high and methyl acetate concentration is very low, the reaction rate equation is then reduced to a first-order with respect to methyl acetate concentration. The first-order model has also been observed from the experimental data obtained in this project for low methyl acetate concentration (less than 1000 ppmv).
Li, Ku-Yen↗
Modeling of a possible conformational change associated with the catalytic mechanism in the hammerhead ribozyme
Here we describe a possible model of the cleavage mechanism in the hammerhead ribozyme. In this model, the 2' hydroxyl of C17 is moved into an appropriate orientation for an in-line attack on the G1.1 phosphate through a change in its sugar pucker from C3' endo to C2' endo. This conformational change in the active site is caused by a change in the uridine turn placing the N2 and N3 atoms of G5 of the conserved core in hydrogen bonding geometry with the N3 and N2 atoms on the conserved G16.2 residue. The observed conformational change in the uridine turn suggests an explanation for the conservation of G5. In the crystal structure of H.M. Pley et al., Nature 372, 68-74 (1994), G5 is situated 5.3A away from G16.2. However, the uridine turn is sufficiently flexible to allow this conformational change with relatively modest changes in the backbone torsion angles (average change of 14.2 degrees). Two magnesium ions were modeled into the active site with positions analogous to those described in the functionally similar Klenow fragment 3'-5' exonuclease (L.S. Beese and T.A. Steitz, EMBO J. 10, 25-33 (1991)), the Group I intron (T.A. Steitz and J.A. Steitz, P.N.A.S. U.S.A. 90, 6498-6502 (1993); R.F. Setlik et al., J. Biomol. Str. Dyn. 10, 945-972 (1993)) and other phosphotransferases. Comparison of this model with one in which the uridine turn conformation was not changed showed that although the changes in the C17 sugar pucker could be modeled, insufficient space existed for the magnesium ions in the active site.
Non-NASA Center↗
Chemical State of Surface Oxygen on Carbon and Its Effects on the Capacity of the Carbon Anode in a Lithium-Ion Battery Investigated
In a lithium-ion battery, the lithium-storage capacity of the carbon anode is greatly affected by a surface layer formed during the first half cycle of lithium insertion and release into and out of the carbon anode. The formation of this solid-electrolyte interface, in turn, is affected by the chemistry of the carbon surface. A study at the NASA Glenn Research Center examined the cause-and-effect relations. Information obtained from this research could contribute in designing a high-capacity lithium-ion battery and, therefore, small, powerful spacecraft. In one test, three types of surfaces were examined: (1) a surface with low oxygen content (1.5 at.%) and a high concentration of active sites, (2) a surface with 4.5 at.% -OH or -OC type oxygen, and (3) a surface with 6.5 at.% O=C type oxygen. The samples were made from the same precursor and had similar bulk properties. They were tested under a constant current of 10 mA/g in half cells that used lithium metal as the counter electrode and 0.5 M lithium iodide in 50/50 (vol%) ethylene carbonate and dimethyl carbonate as the electrolyte. For the first cycle of the electrochemical test, the graph describes the voltage of the carbon anode versus the lithium metal as a function of the capacity (amount of lithium insertion or release). From these data, it can be observed that the surface with low oxygen and a high concentration of active sites could result in a high irreversible capacity. Such a high irreversible capacity could be prevented if the active sites were allowed to react with oxygen in air, producing -OH or -OC type oxygen. The O=C type oxygen, on the other hand, could greatly reduce the capacity of lithium intercalation and, therefore, needs to be avoided during battery fabrication.
Hung, Ching-Cheh↗
Modeling study on the cleavage step of the self-splicing reaction in group I introns
A three-dimensional model of the Tetrahymena thermophila group I intron is used to further explore the catalytic mechanism of the transphosphorylation reaction of the cleavage step. Based on the coordinates of the catalytic core model proposed by Michel and Westhof (Michel, F., Westhof, E. J. Mol. Biol. 216, 585-610 (1990)), we first converted their ligation step model into a model of the cleavage step by the substitution of several bases and the removal of helix P9. Next, an attempt to place a trigonal bipyramidal transition state model in the active site revealed that this modified model for the cleavage step could not accommodate the transition state due to insufficient space. A lowering of P1 helix relative to surrounding helices provided the additional space required. Simultaneously, it provided a better starting geometry to model the molecular contacts proposed by Pyle et al. (Pyle, A. M., Murphy, F. L., Cech, T. R. Nature 358, 123-128. (1992)), based on mutational studies involving the J8/7 segment. Two hydrated Mg2+ complexes were placed in the active site of the ribozyme model, using the crystal structure of the functionally similar Klenow fragment (Beese, L.S., Steitz, T.A. EMBO J. 10, 25-33 (1991)) as a guide. The presence of two metal ions in the active site of the intron differs from previous models, which incorporate one metal ion in the catalytic site to fulfill the postulated roles of Mg2+ in catalysis. The reaction profile is simulated based on a trigonal bipyramidal transition state, and the role of the hydrated Mg2+ complexes in catalysis is further explored using molecular orbital calculations.
NASA Discipline Exobiology↗
The Role of Composition and Surface Area Variability in Ice Nucleation, and How to Get Rid of It
Ice nucleation active site densities and nucleation rates are commonly determined by measuring the fraction of droplets that freeze at different temperatures. In analysing these experiments it is commonly assumed that variability in the immersed particle surface area and composition within a sample can be neglected, allowing a simple parameterization of ice nucleation efficiencies. Here it is shown that these approximations may result in large error, and translate into a bias in estimated active site densities of about six orders of magnitude. When applied in cloud models it may represent up to 5 K error in cloud glaciation temperature. A solution to this enduring problem is proposed for the first time. It is shown that by performing droplet freezing experiments varying mean particle surface area along with the temperature such a bias can be quantitatively removed. This amounts to differentiating the "freezing rate'' from the ice nucleation coefficient, or, the apparent and the actual active site density of a material. The proposed method will contribute to reduce existing uncertainties in the relative strength of the ice nucleation ability of different aerosol species, and the modeling of mixed-phase clouds.
Barahona, Donifan↗