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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.

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At least 523 records · Page 29
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Single-molecule diffusometry reveals no catalysis-induced diffusion enhancement of alkaline phosphatase as proposed by FCS experiments

Significance Recent experiments have suggested that the energy released by a chemical reaction can propel its enzyme catalyst (for example, alkaline phosphatase). However, this topic remains controversial, partially due to the indirect and ensemble nature of existing measurements. Here, we used recently developed single-molecule approaches to monitor directly the motions of individual proteins in aqueous solution and find that single alkaline phosphatase enzymes do not diffuse faster under catalysis. Instead, we demonstrate that interactions between the fluorescent dye and the enzyme’s substrate can produce the signature of apparent diffusion enhancement in fluorescence correlation spectroscopy, the standard ensemble assay currently used to study enzyme diffusion and indicate that single-molecule approaches provide a more robust means to investigate diffusion at the nanoscale.

36 MATERIALS SCIENCE↗
DOE OSTI2016

Large Conformational Changes of Insertion 3 in Human Glycyl-tRNA Synthetase (hGlyRS) during Catalysis

Glycyl-tRNA synthetase (GlyRS) is the enzyme that covalently links glycine to cognate tRNA for translation. It is of great interest because of its nonconserved quaternary structures, unique species-specific aminoacylation properties, and noncanonical functions in neurological diseases, but none of these is fully understood. We report two crystal structures of human GlyRS variants, in the free form and in complex with tRNA Gly respectively, and reveal new aspects of the glycylation mechanism. We discover that insertion 3 differs considerably in conformation in catalysis and that it acts like a "switch" and fully opens to allow tRNA to bind in a cross-subunit fashion. The flexibility of the protein is supported by molecular dynamics simulation, as well as enzymatic activity assays. The biophysical and biochemical studies suggest that human GlyRS may utilize its flexibility for both the traditional function (regulate tRNA binding) and alternative functions (roles in diseases).

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Caught in motion: human NTHL1 undergoes interdomain rearrangement necessary for catalysis

Abstract Base excision repair (BER) is the main pathway protecting cells from the continuous damage to DNA inflicted by reactive oxygen species. BER is initiated by DNA glycosylases, each of which repairs a particular class of base damage. NTHL1, a bifunctional DNA glycosylase, possesses both glycolytic and β-lytic activities with a preference for oxidized pyrimidine substrates. Defects in human NTHL1 drive a class of polyposis colorectal cancer. We report the first X-ray crystal structure of hNTHL1, revealing an open conformation not previously observed in the bacterial orthologs. In this conformation, the six-helical barrel domain comprising the helix-hairpin-helix (HhH) DNA binding motif is tipped away from the iron sulphur cluster-containing domain, requiring a conformational change to assemble a catalytic site upon DNA binding. We found that the flexibility of hNTHL1 and its ability to adopt an open configuration can be attributed to an interdomain linker. Swapping the human linker sequence for that of Escherichia coli yielded a protein chimera that crystallized in a closed conformation and had a reduced activity on lesion-containing DNA. This large scale interdomain rearrangement during catalysis is unprecedented for a HhH superfamily DNA glycosylase and provides important insight into the molecular mechanism of hNTHL1.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Structural characterization of Class 2 OLD family nucleases supports a two-metal catalysis mechanism for cleavage

Overcoming lysogenization defect (OLD) proteins constitute a family of uncharacterized nucleases present in bacteria, archaea, and some viruses. These enzymes contain an N-terminal ATPase domain and a C-terminal Toprim domain common amongst replication, recombination, and repair proteins. The in vivo activities of OLD proteins remain poorly understood and no definitive structural information exists. Here we identify and define two classes of OLD proteins based on differences in gene neighborhood and amino acid sequence conservation and present the crystal structures of the catalytic C-terminal regions from the Burkholderia pseudomallei and Xanthamonas campestris p.v. campestris Class 2 OLD proteins at 2.24 Å and 1.86 Å resolution respectively. The structures reveal a two-domain architecture containing a Toprim domain with altered architecture and a unique helical domain. Conserved side chains contributed by both domains coordinate two bound magnesium ions in the active site of B. pseudomallei OLD in a geometry that supports a two-metal catalysis mechanism for cleavage. The spatial organization of these domains additionally suggests a novel mode of DNA binding that is distinct from other Toprim containing proteins. Together, these findings define the fundamental structural properties of the OLD family catalytic core and the underlying mechanism controlling nuclease activity.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Lattice field theory study of magnetic catalysis in graphene

We discuss the simulation of the low-energy effective field theory (EFT) for graphene in the presence of an external magnetic field. Our fully nonperturbative calculation uses methods of lattice gauge theory to study the theory using a hybrid Monte Carlo approach. We investigate the phenomenon of magnetic catalysis in the context of graphene by studying the chiral condensate which is the order parameter characterizing the spontaneous breaking of chiral symmetry. In the EFT, the symmetry breaking pattern is given by $U(4) \to U(2) \times U(2)$. We also comment on the difficulty, in this lattice formalism, of studying the time-reversal-odd condensate characterizing the ground state in the presence of a magnetic field. Lastly, we study the mass spectrum of the theory, in particular the Nambu-Goldstone (NG) mode as well as the Dirac quasiparticle, which is predicted to obtain a dynamical mass.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Ensemble-function relationships to dissect mechanisms of enzyme catalysis

Decades of structure-function studies have established our current extensive understanding of enzymes. However, traditional structural models are snapshots of broader conformational ensembles of interchanging states. We demonstrate the need for conformational ensembles to understand function, using the enzyme ketosteroid isomerase (KSI) as an example. Comparison of prior KSI cryogenic x-ray structures suggested deleterious mutational effects from a misaligned oxyanion hole catalytic residue. However, ensemble information from room-temperature x-ray crystallography, combined with functional studies, excluded this model. Ensemble-function analyses can deconvolute effects from altering the probability of occupying a state (P-effects) and changing the reactivity of each state (k-effects); our ensemble-function analyses revealed functional effects arising from weakened oxyanion hole hydrogen bonding and substrate repositioning within the active site. Ensemble-function studies will have an integral role in understanding enzymes and in meeting the future goals of a predictive understanding of enzyme catalysis and engineering new enzymes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2017

Evolutionary drivers of thermoadaptation in enzyme catalysis

With early life likely to have existed in a hot environment, enzymes had to cope with an inherent drop in catalytic speed caused by lowered temperature. Here we characterize the molecular mechanisms underlying thermoadaptation of enzyme catalysis in adenylate kinase using ancestral sequence reconstruction spanning 3 billion years of evolution. We show that evolution solved the enzyme’s key kinetic obstacle—how to maintain catalytic speed on a cooler Earth—by exploiting transition-state heat capacity. Tracing the evolution of enzyme activity and stability from the hot-start toward modern hyperthermophilic, mesophilic, and psychrophilic organisms illustrates active pressure versus passive drift in evolution on a molecular level, refutes the debated activity/stability trade-off, and suggests that the catalytic speed of adenylate kinase is an evolutionary driver for organismal fitness.

58 GEOSCIENCES↗
DOE OSTI2016

Structures of Pathogenic Fungal FKBP12s Reveal Possible Self-Catalysis Function

Invasive fungal infections remain difficult to treat and require novel targeting strategies. The 12-kDa FK506-binding protein (FKBP12) is a ubiquitously expressed peptidyl-prolyl isomerase with considerable homology between fungal pathogens and is thus a prime candidate for future targeting efforts to generate a panfungal strategy. Despite decades of research on FKBPs, their substrates and mechanisms of action remain unclear. Here we describe structural, biochemical, and in vivo analyses of FKBP12s from the pathogenic fungi Candida albicans, Candida glabrata, and Aspergillus fumigatus. Strikingly, multiple apo A. fumigatus and C. albicans FKBP12 crystal structures revealed a symmetric, intermolecular interaction involving the deep insertion of an active-site loop proline into the active-site pocket of an adjacent subunit. Such interactions have not been observed in previous FKBP structures. This finding indicates the possibility that this is a self-substrate interaction unique to the A. fumigatus and C. albicans fungal proteins that contain this central proline. Structures obtained with the proline in the cis and trans states provide more data in support of self-catalysis. Moreover, cysteine cross-linking experiments captured the interacting dimer, supporting the idea that it forms in solution. Finally, genetic studies exploring the impact of mutations altering the central proline and an adjacent residue provide evidence that any dimeric state formed in vivo, where FKBP12 concentrations are low, is transient. Taken together, these findings suggest a unique mechanism of self-substrate regulation by fungal FKBP12s, lending further novel understanding of this protein for future drug-targeting efforts.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Experimental and theoretical insights into the effects of pH on catalysis of bond-cleavage by the lignin peroxidase isozyme H8 from Phanerochaete chrysosporium

Abstract Background Lignin peroxidases catalyze a variety of reactions, resulting in cleavage of both β-O-4′ ether bonds and C–C bonds in lignin, both of which are essential for depolymerizing lignin into fragments amendable to biological or chemical upgrading to valuable products. Studies of the specificity of lignin peroxidases to catalyze these various reactions and the role reaction conditions such as pH play have been limited by the lack of assays that allow quantification of specific bond-breaking events. The subsequent theoretical understanding of the underlying mechanisms by which pH modulates the activity of lignin peroxidases remains nascent. Here, we report on combined experimental and theoretical studies of the effect of pH on the enzyme-catalyzed cleavage of β-O-4′ ether bonds and of C–C bonds by a lignin peroxidase isozyme H8 from Phanerochaete chrysosporium and an acid stabilized variant of the same enzyme. Results Using a nanostructure initiator mass spectrometry assay that provides quantification of bond breaking in a phenolic model lignin dimer we found that catalysis of degradation of the dimer to products by an acid-stabilized variant of lignin peroxidase isozyme H8 increased from 38.4% at pH 5 to 92.5% at pH 2.6. At pH 2.6, the observed product distribution resulted from 65.5% β-O-4′ ether bond cleavage, 27.0% C α -C 1 carbon bond cleavage, and 3.6% C α -oxidation as by-product. Using ab initio molecular dynamic simulations and climbing-image Nudge Elastic Band based transition state searches, we suggest the effect of lower pH is via protonation of aliphatic hydroxyl groups under which extremely acidic conditions resulted in lower energetic barriers for bond-cleavages, particularly β-O-4′ bonds. Conclusion These coupled experimental results and theoretical explanations suggest pH is a key driving force for selective and efficient lignin peroxidase isozyme H8 catalyzed depolymerization of the phenolic lignin dimer and further suggest that engineering of lignin peroxidase isozyme H8 and other enzymes involved in lignin depolymerization should include targeting stability at low pH.

09 BIOMASS FUELS↗
DOE OSTI2012

Mechanistic Studies at the Interface Between Organometallic Chemistry and Homogeneous Catalysis

Our goal was to learn the intimate mechanistic details of reactions involved in homogeneous catalysis and to use the insight we gain to develop new and improved catalysts. Our work centered on the hydrogenation of polar functional groups such as aldehydes and ketones and on hydroformylation. Specifically, we concentrated on catalysts capable of simultaneously transferring hydride from a metal center and a proton from an acidic oxygen or nitrogen center to an aldehyde or ketone. An economical iron based catalyst was developed and patented. Better understanding of fundamental organometallic reactions and catalytic processes enabled design of energy and material efficient chemical processes. Our work contributed to the development of catalysts for the selective and mild hydrogenation of ketones and aldehydes; this will provide a modern green alternative to reductions by LiAlH 4 and NaBH 4 , which require extensive work-up procedures and produce waste streams.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2011

Charge Transfer and Support Effects in Heterogeneous Catalysis

The kinetic, electronic and spectroscopic properties of two-dimensional oxide-supported catalysts were investigated in order to understand the role of charge transfer in catalysis. Pt/TiO 2 nanodiodes were fabricated and used as catalysts for hydrogen oxidation. During the reaction, the current through the diode, as well as its I-V curve, were monitored, while gas chromatography was used to measure the reaction rate. The current and the turnover rate were found to have the same temperature dependence, indicating that hydrogen oxidation leads to the non-adiabatic excitation of electrons in Pt. A fraction of these electrons have enough energy to ballistically transport through Pt and overcome the Schottky barrier at the interface with TiO 2 . The yield for this phenomenon is on the order of 10 -4 electrons per product molecule formed, similar to what has been observed for CO oxidation and for the adsorption of many different molecules. The same Pt/TiO 2 system was used to compare currents in hydrogen oxidation and deuterium oxidation. The current through the diode under deuterium oxidation was found to be greater than under hydrogen oxidation by a factor of three. Weighted by the difference in turnover frequencies for the two isotopes, this would imply a chemicurrent yield 5 times greater for D 2 compared to H 2 , contrary to what is expected given the higher mass of D 2 . Reversible changes in the rectification factor of the diode are observed when switching between D 2 and H 2 . These changes are a likely cause for the differences in current between the two isotopes. In the nanodiode experiments, surface chemistry leads to charge flow, suggesting the possibility of creating charge flow to tune surface chemistry. This was done first by exposing a Pt/Si diode to visible light while using it as a catalyst for H 2 oxidation. Absorption of the light in the Si, combined with the band bending at the interface, gives rise to a steady-state flow of hot holes to the surface. This leads to a decrease in turnover on the surface, an effect which is enhanced when a reverse bias is applied to the diode. Similar experiments were carried out for CO oxidation. On Pt/Si diodes, the reaction rate was found to increase when a forward bias was applied. When the diode was exposed to visible light and a reverse bias was applied, the rate was instead decreased. This implies that a flow of negative charges to the surface increases turnover, while positive charges decrease it. Charge flow in an oxide supported metal catalyst can be modified even without designing the catalyst as a solid state electronic device. This was done by doping stoichiometric and nonstoichiometric TiO 2 films with F, and using the resulting oxides as supports for Pt films. In the case of stoichiometric TiO 2 , F was found to act as an n-type dopant, creating a population of filled electronic states just below the conduction band, and dramatically increasing the conductivity of the oxide film. The electrons in those states can transfer to surface O, activating it for reaction with CO, and leading to increased turnover for CO oxidation. This reinforces the hypothesis that CO oxidation is activated by a flow of negative charges to the surface. The same set of catalysts was used for methanol oxidation. The electronic properties of the TiO 2 films again correlated with the turnover rates, but also with selectivity. With stoichiometric TiO 2 as the support, F-doping caused an increase in selectivity toward the formation of partial oxidation products, formaldehyde and methyl formate, versus the total oxidation product, CO 2 . With non-stoichiometric TiO 2 , F-doping had the reverse effect. Ambient Pressure X-Ray Photoelectron Spectroscopy was used to investigate this F-doping effect in reaction conditions. In O 2 alone, and in CO oxidation conditions, the O1s spectrum showed a high binding energy peak that correlated in intensity with the activity of the different films: for stoichiometric films, the peak decreased in intensity with F-doping, while for nonstoichiometric films, the opposite was observed. No such changes were visible in the C1s spectrum, confirming the role of O activation in the reaction. This thesis adds to the body of knowledge on the importance of charge transfer at the metal-oxide interface in shaping the reactivity of heterogeneous catalysts, and provides examples of how this can be the basis for new methods to tune reactivity.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2012

Enhanced Micellar Catalysis LDRD.

The primary goals of the Enhanced Micellar Catalysis project were to gain an understanding of the micellar environment of DF-200, or similar liquid CBW surfactant-based decontaminants, as well as characterize the aerosolized DF-200 droplet distribution and droplet chemistry under baseline ITW rotary atomization conditions. Micellar characterization of limited surfactant solutions was performed externally through the collection and measurement of Small Angle X-Ray Scattering (SAXS) images and Cryo-Transmission Electron Microscopy (cryo-TEM) images. Micellar characterization was performed externally at the University of Minnesota s Characterization Facility Center, and at the Argonne National Laboratory Advanced Photon Source facility. A micellar diffusion study was conducted internally at Sandia to measure diffusion constants of surfactants over a concentration range, to estimate the effective micelle diameter, to determine the impact of individual components to the micellar environment in solution, and the impact of combined components to surfactant phase behavior. Aerosolized DF-200 sprays were characterized for particle size and distribution and limited chemical composition. Evaporation rates of aerosolized DF-200 sprays were estimated under a set of baseline ITW nozzle test system parameters.

Betty, Rita G.↗
DOE OSTI2012

Charge Transfer and Catalysis at the Metal Support Interface

Kinetic, electronic, and spectroscopic characterization of model Pt–support systems are used to demonstrate the relationship between charge transfer and catalytic activity and selectivity. The results show that charge flow controls the activity and selectivity of supported metal catalysts. This dissertation builds on extensive existing knowledge of metal–support interactions in heterogeneous catalysis. The results show the prominent role of charge transfer at catalytic interfaces to determine catalytic activity and selectivity. Further, this research demonstrates the possibility of selectively driving catalytic chemistry by controlling charge flow and presents solid-state devices and doped supports as novel methods for obtaining electronic control over catalytic reaction kinetics.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2016

Active sites engineering of metal-organic frameworks for heterogeneous catalysis

In conclusion, we have for the first time developed a novel solid base catalyst, Ndoped MOF-253 derived porous carbons (Cz-MOF-253). Cz-MOF-253 is highly porous and exhibit high efficiency in Knoevenagel condensation reaction. Furthermore, Cz-MOF-253 is robust and can be reused up to five times. In comparison, the analogous nitrogen-free catalyst-Cz-DUT-5, and other nitrogen- MOFs derived carbon showed an inferior performance. Moreover, the high basicity and porous nature enable the design of bifunctional catalyst and facilitate tandem condensation-hydrogenation reactions. This work delineates the first attempt that demonstrates MOF-derived carbons as solid base catalyst and its potential application in tandem catalysis. Future work on exploring new catalytic reactions based on such porous Lewis basic MOF-derived carbons is currently underway.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2017

Catalysis, dynamics and stability of enzymes under extreme conditions

This project led to an unprecedented understanding of how enzymes can catalyze chemical reactions with such high catalytic turnover numbers. This was achieved by a detailed description of the free energy landscape of adenylate kinase using a combination of experimental atomic resolution techniques and computation. In this project, a systematic approach was developed how to characterize free energy landscapes with these biophysical methods. These approaches are directly transferable to other enzymes. In addition, we recreated the evolutionary pathway of enzyme evolution over about 3.5 billion years. The results shed light into how enzymes adapted to the decrease in temperature by increasing their catalytic power at lower temperatures. The data demonstrate fundamental principles of evolution such as active pressure versus passive drift. The adaptation of biocatalyst to extreme conditions such as high or low temperature, pressure (living deep at sea) or high salt was studied. Lessons learned from this project have major implications for catalysis in biotechnology.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2018

Studies of Metal-Metal Bonded Compounds in Catalysis

The overall goals of this research are (1) to define the fundamental coordination chemistry underlying successful catalytic transformations promoted by metal-metal bonded compounds, and (2) to explore new chemical transformations that occur at metal-metal bonded sites that could lead to the discovery of new catalytic processes. Transformations of interest include metal-promoted reactions of carbene, nitrene, or nitrido species to yield products with new C–C and C–N bonds, respectively. The most promising suite of transition metal catalysts for these transformations is the set of metal-metal bonded coordination compounds of Ru and Rh of the general formula M 2 (ligand) 4 , where M = Ru or Rh and ligand = a monoanionic, bridging ligand such as acetate. Development of new catalysts and improvement of catalytic conditions have been stymied by a general lack of knowledge about the nature of highly reactive intermediates in these reactions, the knowledge that is to be supplied by this work. Our three specific objectives for this year have been (A) to trap, isolate, and characterize new reactive intermediates of general relevance to catalysis, (B) to explore the electronic structure and reactivity of these unusual species, and how these two properties are interrelated, and (C) to use our obtained mechanistic knowledge to design new catalysts with a focus on Earth-abundant first-row transition metal compounds.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗