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At least 1,099 records · Page 61
All sourcesNASA NTRSDOE OSTI
DOE OSTI2018

Perspective: Size selected clusters for catalysis and electrochemistry

We report that size-selected clusters containing a handful of atoms may possess noble catalytic properties different from nano-sized or bulk catalysts. Size- and composition-selected clusters can also serve as models of the catalytic active site, where an addition or removal of a single atom can have a dramatic effect on their activity and selectivity. In this Perspective, we provide an overview of studies performed under both ultra-high vacuum and realistic reaction conditions aimed at the interrogation, characterization and understanding of the performance of supported size-selected clusters in heterogeneous and electrochemical reactions, which address the effects of cluster size, cluster composition, cluster-support interactions and reaction conditions, the key parameters for the understanding and control of catalyst functionality. Computational modelling based on density functional theory sampling of local minima and energy barriers or ab initio Molecular Dynamics simulations is an integral part of this research by providing fundamental understanding of the catalytic processes at the atomic level, as well as by predicting new materials compositions which can be validated in experiments. Lastly, we discuss approaches which aim at the scale up of the production of well-defined clusters for use in real world applications.

36 MATERIALS SCIENCE↗
DOE OSTI2024

The physical chemistry of solar fuels catalysis

The demonstration of effective light-driven electrochemical water splitting at the surface of a TiO 2 electrode in the seminal 1972 Honda–Fujishima publication spurred global research efforts to understand this effect and design advanced systems for solar H 2 generation from water as a carbon-free and sustainable fuel. In the 50+ years since that discovery, research investigating approaches toward the catalytic generation of the so-called “solar fuels,” i.e., not only H 2 from water but also CO 2 reduction products and NH 3 from N 2 , has expanded dramatically in scope and scale. The development of new experimental and computational methods and construction and commissioning of large-scale facilities have paved the way for important insights into the machinery of natural photosynthesis, leading to a greater understanding of the complexity of light-to-chemical energy conversion with an exquisite temporal and spatial resolution. Finally, these studies have provided the foundation for biologically inspired molecular and hybrid designs with the goal to promote the photochemical steps critical to solar fuels generation while avoiding unproductive or unnecessary pathways.

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

Structures of trehalose-6-phosphate phosphatase from pathogenic fungi reveal the mechanisms of substrate recognition and catalysis

Trehalose is a disaccharide essential for the survival and virulence of pathogenic fungi. The biosynthesis of trehalose requires trehalose-6-phosphate synthase, Tps1, and trehalose-6-phosphate phosphatase, Tps2. Here, we report the structures of the N-terminal domain of Tps2 (Tps2NTD) from Candida albicans , a transition-state complex of the Tps2 C-terminal trehalose-6-phosphate phosphatase domain (Tps2PD) bound to BeF 3 and trehalose, and catalytically dead Tps2PD(D24N) from Cryptococcus neoformans bound to trehalose-6-phosphate (T6P). The Tps2NTD closely resembles the structure of Tps1 but lacks any catalytic activity. The Tps2PD–BeF 3 –trehalose and Tps2PD(D24N)–T6P complex structures reveal a “closed” conformation that is effected by extensive interactions between each trehalose hydroxyl group and residues of the cap and core domains of the protein, thereby providing exquisite substrate specificity. Disruption of any of the direct substrate–protein residue interactions leads to significant or complete loss of phosphatase activity. Notably, the Tps2PD–BeF 3 –trehalose complex structure captures an aspartyl-BeF 3 covalent adduct, which closely mimics the proposed aspartyl-phosphate intermediate of the phosphatase catalytic cycle. Structures of substrate-free Tps2PD reveal an “open” conformation whereby the cap and core domains separate and visualize the striking conformational changes effected by substrate binding and product release and the role of two hinge regions centered at approximately residues 102–103 and 184–188. Significantly, tps2 Δ, tps2NTD Δ, and tps2D705N strains are unable to grow at elevated temperatures. Combined, these studies provide a deeper understanding of the substrate recognition and catalytic mechanism of Tps2 and provide a structural basis for the future design of novel antifungal compounds against a target found in three major fungal pathogens.

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

Substrate recognition and catalysis by GH47 α-mannosidases involved in Asn-linked glycan maturation in the mammalian secretory pathway

Maturation of Asn-linked oligosaccharides in the eukaryotic secretory pathway requires the trimming of nascent glycan chains to remove all glucose and several mannose residues before extension into complex-type structures on the cell surface and secreted glycoproteins. Multiple glycoside hydrolase family 47 (GH47) α-mannosidases, including endoplasmic reticulum (ER) α-mannosidase I (ERManI) and Golgi α-mannosidase IA (GMIA), are responsible for cleavage of terminal α1,2-linked mannose residues to produce uniquely trimmed oligomannose isomers that are necessary for ER glycoprotein quality control and glycan maturation. ERManI and GMIA have similar catalytic domain structures, but each enzyme cleaves distinct residues from tribranched oligomannose glycan substrates. The structural basis for branch-specific cleavage by ERManI and GMIA was explored by replacing an essential enzyme-bound Ca 2+ ion with a lanthanum (La 3+ ) ion. This ion swap led to enzyme inactivation while retaining high-affinity substrate interactions. Cocrystallization of La 3+ -bound enzymes with Man9GlcNAc 2 substrate analogs revealed enzyme–substrate complexes with distinct modes of glycan branch insertion into the respective enzyme active-site clefts. Both enzymes had glycan interactions that extended across the entire glycan structure, but each enzyme engaged a different glycan branch and used different sets of glycan interactions. Additional mutagenesis and time-course studies of glycan cleavage probed the structural basis of enzyme specificity. Here, the results provide insights into the enzyme catalytic mechanisms and reveal structural snapshots of the sequential glycan cleavage events. The data also indicate that full steric access to glycan substrates determines the efficiency of mannose-trimming reactions that control the conversion to complex-type structures in mammalian cells.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Interplay of catalysis, fidelity, threading, and processivity in the exo- and endonucleolytic reactions of human exonuclease I

Human exonuclease 1 (hExo1) is a member of the RAD2/XPG structure-specific 5'-nuclease superfamily. Its dominant, processive 5'–3' exonuclease and secondary 5'-flap endonuclease activities participate in various DNA repair, recombination, and replication processes. A single active site processes both recessed ends and 5'-flap substrates. By initiating enzyme reactions in crystals, we have trapped hExo1 reaction intermediates that reveal structures of these substrates before and after their exo- and endonucleolytic cleavage, as well as structures of uncleaved, unthreaded, and partially threaded 5' flaps. Their distinctive 5' ends are accommodated by a small, mobile arch in the active site that binds recessed ends at its base and threads 5' flaps through a narrow aperture within its interior. A sequence of successive, interlocking conformational changes guides the two substrate types into a shared reaction mechanism that catalyzes their cleavage by an elaborated variant of the two-metal, in-line hydrolysis mechanism. Coupling of substrate-dependent arch motions to transition-state stabilization suppresses inappropriate or premature cleavage, enhancing processing fidelity. Furthermore, the striking reduction in flap conformational entropy is catalyzed, in part, by arch motions and transient binding interactions between the flap and unprocessed DNA strand. At the end of the observed reaction sequence, hExo1 resets without relinquishing DNA binding, suggesting a structural basis for its processivity.

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

Metal-free class Ie ribonucleotide reductase from pathogens initiates catalysis with a tyrosine-derived dihydroxyphenylalanine radical

All cells obtain 2'-deoxyribonucleotides for DNA synthesis through the activity of a ribonucleotide reductase (RNR). The class I RNRs found in humans and pathogenic bacteria differ in ( i ) use of Fe(II), Mn(II), or both for activation of the dinuclear-metallocofactor subunit, β; ( ii ) reaction of the reduced dimetal center with dioxygen or superoxide for this activation; ( iii ) requirement (or lack thereof) for a flavoprotein activase, NrdI, to provide the superoxide from O 2 ; and ( iv ) use of either a stable tyrosyl radical or a high-valent dimetal cluster to initiate each turnover by oxidizing a cysteine residue in the α subunit to a radical (Cys•). The use of manganese by bacterial class I, subclass b-d RNRs, which contrasts with the exclusive use of iron by the eukaryotic Ia enzymes, appears to be a countermeasure of certain pathogens against iron deprivation imposed by their hosts. Here, we report a metal-free type of class I RNR (subclass e) from two human pathogens. The Cys• in its α subunit is generated by a stable, tyrosine-derived dihydroxyphenylalanine radical (DOPA•) in β. The three-electron oxidation producing DOPA• occurs in Escherichia coli only if the β is coexpressed with the NrdI activase encoded adjacently in the pathogen genome. We conclude the independence of this new RNR from transition metals, or the requirement for a single metal ion only transiently for activation, may afford the pathogens an even more potent countermeasure against transition metal-directed innate immunity.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Crossing the bridge from molecular catalysis to a heterogenous electrode in electrocatalytic water oxidation

Significant progress has been made in designing single-site molecular Ru(II)-polypyridyl-aqua catalysts for homogenous catalytic water oxidation. Surface binding and transfer of the catalytic reactivity onto conductive substrates provides a basis for heterogeneous applications in electrolytic cells and dye-sensitized photoelectrosynthesis cells (DSPECs). Earlier efforts have focused on phosphonic acid (-PO 3 H 2 ) or carboxylic acid (-CO 2 H) bindings on oxide surfaces. However, issues remain with limited surface stabilities, especially in aqueous solutions at higher pH under conditions that favor water oxidation by reducing the thermodynamic barrier and accelerating the catalytic rate using atom-proton transfer (APT) pathways. Here, we address the problem by combining silane surface functionalization and surface reductive electropolymerization on mesoporous, nanofilms of indium tin oxide (ITO) on fluorine-doped tin oxide (FTO) substrates (FTO| nano ITO). FTO| nano ITO electrodes were functionalized with vinyltrimethoxysilane (VTMS) to introduce vinyl groups on the electrode surfaces by silane attachment, followed by surface electropolymerization of the vinyl-derivatized complex, [Ru II (Mebimpy)(dvbpy)(OH 2 )] 2+ (1 2+ ; Mebimpy: 2,6-bis(1-methyl-1 H -benzo[ d ]imidazol-2-yl)pyridine; dvbpy: 5,5'-divinyl-2,2'-bipyridine), in a mechanism dominated by a grafting-through method. The surface coverage of catalyst 1 2+ was controlled by the number of electropolymerization cycles. The combined silane attachment/cross-linked polymer network stabilized 1 2+ on the electrode surface under a variety of conditions especially at pH > ~6. Surface-grafted poly1 2+ was stable toward redox cycling at pH ~ 7.5 over an ~4-h period. Finally, sustained heterogeneous electrocatalytic water oxidation by the electrode gave steady-state currents for at least ~6 h with a Faradaic efficiency of ~68% for O 2 production.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Selective cysteine-to-selenocysteine changes in a [NiFe]-hydrogenase confirm a special position for catalysis and oxygen tolerance

Significance Substitution of cysteine by selenocysteine is held responsible for the increased performance of many enzymes: The higher activity of [NiFeSe]-hydrogenases compared with their [NiFe] counterparts is often attributed to the Sec replacement of one active-site cysteine ligand. Replacing each of the four active-site cysteine residues in an O 2 -tolerant [NiFe]-hydrogenase by selenocysteine shows that this substitution alone does not overcome the inability to evolve H 2 that is a characteristic of the group 1d hydrogenases. A nonbridging cysteine lying on the direct path between the Ni and an adjacent proton-relaying glutamic acid emerges as being very special: Its substitution by selenocysteine confers extreme tolerance to O 2 but disrupts the proton transfer pathway, providing an example of where sulfur is superior to selenium.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Operando 3D imaging of defects dynamics of twinned-nanocrystal during catalysis

Using operando Bragg coherent x-ray diffraction imaging, we visualised three-dimensionally a single twinned-gold nanocrystal during the CO oxidation reaction. We describe the defect dynamics process occurring under operating conditions and indicate the correlation between the nucleation of highly strained regions at the surface of the nanocrystal and its catalytic activity. Understanding the twinning deformation mechanism sheds light on the creation of active sites, and could well contribute to the understanding of the catalytic behaviour of other catalysts. Furthermore, with the start-up of 4th generation synchrotron sources, we anticipate that coherent hard x-ray diffraction imaging techniques will play a major role in imaging in situ chemical processes.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2017

Dark catalysis

Recently it was shown that dark matter with mass of order the weak scale can be charged under a new long-range force, decoupled from the Standard Model, with only weak constraints from early Universe cosmology. Here we consider the implications of an additional charged particle C that is light enough to lead to significant dissipative dynamics on galactic times scales. We highlight several novel features of this model, which can be relevant even when the C particle constitutes only a small fraction of the number density (and energy density). We assume a small asymmetric abundance of the C particle whose charge is compensated by a heavy X particle so that the relic abundance of dark matter consists mostly of symmetric X and X-bar , with a small asymmetric component made up of X and C . As the universe cools, it undergoes asymmetric recombination binding the free C s into ( XC ) dark atoms efficiently. Even with a tiny asymmetric component, the presence of C particles catalyzes tight coupling between the heavy dark matter X and the dark photon plasma that can lead to a significant suppression of the matter power spectrum on small scales and lead to some of the strongest bounds on such dark matter theories. We find a viable parameter space where structure formation constraints are satisfied and significant dissipative dynamics can occur in galactic haloes but show a large region is excluded. Our model shows that subdominant components in the dark sector can dramatically affect structure formation.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2024

BBN catalysis by doubly charged particles

Abstract We consider primordial nucleosynthesis in the presence of hypotheticalquasi-stable doubly charged particles. Existence ofX –– withmacroscopic lifetimes will lead to the formation of its bound states with 4 He and otherlight elements, significantly facilitating the subsequentformation of lithium nuclei. From observational constraints on maximumallowable amount of lithium, that we update in this work, we derivestrong constraints on the abundance and lifetime ofX –– . In alikely cosmological freeze-out scenario with temperatures initiallyexceeding the mass ofX –– , the BBN constrains the lifetime of theseparticles to be less than about 100 seconds. For parametrically longlifetimes, lithium abundance data constrainX –– abundance to be lessthan 10 -9 relative to protons, regardless of whether these particlesdecay or remain stable. Stable particles could saturate the dark matterdensity only if their mass is comparable to or in excess of10 10 GeV, and most ofX –– will be found in bound states withberyllium nuclei, so that chemically they would appear as abnormallyheavy helium isotopes.

Astronomy & Astrophysics↗