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At least 145 records · Page 8

Rapid selective sweep of pre-existing polymorphisms and slow fixation of new mutations in experimental evolution of Desulfovibrio vulgaris

To investigate the genetic basis of microbial evolutionary adaptation to salt (NaCl) stress, populations of Desulfovibrio vulgaris Hildenborough (DvH), a sulfate-reducing bacterium important for the biogeochemical cycling of sulfur, carbon and nitrogen, and potentially the bioremediation of toxic heavy metals and radionuclides, were propagated under salt stress or non-stress conditions for 1200 generations. Whole-genome sequencing revealed 11 mutations in salt stress-evolved clone ES9-11 and 14 mutations in non-stress-evolved clone EC3-10. Whole-population sequencing data suggested the rapid selective sweep of the pre-existing polymorphisms under salt stress within the first 100 generations and the slow fixation of new mutations. Population genotyping data demonstrated that the rapid selective sweep of pre-existing polymorphisms was common in salt stress-evolved populations. In contrast, the selection of pre-existing polymorphisms was largely random in EC populations. Consistently, at 100 generations, stress-evolved population ES9 showed improved salt tolerance, namely increased growth rate (2.0-fold), higher biomass yield (1.8-fold) and shorter lag phase (0.7-fold) under higher salinity conditions. The beneficial nature of several mutations was confirmed by site-directed mutagenesis. All four tested mutations contributed to the shortened lag phases under higher salinity condition. In particular, compared with the salt tolerance improvement in ES9-11, a mutation in a histidine kinase protein gene lytS contributed 27% of the growth rate increase and 23% of the biomass yield increase while a mutation in hypothetical gene DVU2472 contributed 24% of the biomass yield increase. Our results suggested that a few beneficial mutations could lead to dramatic improvements in salt tolerance.

Zhou, Aifen↗

Hydrogen-bearing iron peroxide and the origin of ultralow-velocity zones

Ultralow-velocity zones (ULVZs) at Earth’s core–mantle boundary region have important implications for the chemical composition and thermal structure of our planet, but their origin has long been debated. Hydrogen-bearing iron peroxide (FeO 2 H x ) in the pyrite-type crystal structure was recently found to be stable under the conditions of the lowermost mantle. Using high-pressure experiments and theoretical calculations, we find that iron peroxide with a varying amount of hydrogen has a high density and high Poisson ratio as well as extremely low sound velocities consistent with ULVZs. Here in this paper we also report a reaction between iron and water at 86 gigapascals and 2,200 kelvin that produces FeO 2 H x . This would provide a mechanism for generating the observed volume occupied by ULVZs through the reaction of about one-tenth the mass of Earth’s ocean water in subducted hydrous minerals with the effectively unlimited reservoir of iron in Earth’s core. Unlike other candidates for the composition of ULVZs, FeO 2 H x synthesized from the superoxidation of iron by water would not require an extra transportation mechanism to migrate to the core–mantle boundary. These dense FeO2Hx-rich domains would be expected to form directly in the core–mantle boundary region and their properties would provide an explanation for the many enigmatic seismic features that are observed in ULVZs

58 GEOSCIENCES↗

Sterically controlled mechanochemistry under hydrostatic pressure

Mechanical stimuli can modify the energy landscape of chemical reactions and enable reaction pathways, offering a synthetic strategy that complements conventional chemistry. These mechanochemical mechanisms have been studied extensively in one-dimensional polymers under tensile stress using ring-opening and reorganization, polymer unzipping and disulfide reduction as model reactions. In these systems, the pulling force stretches chemical bonds, initiating the reaction. Additionally, it has been shown that forces orthogonal to the chemical bonds can alter the rate of bond dissociation. Furthermore, these bond activation mechanisms have not been possible under isotropic, compressive stress (that is, hydrostatic pressure). Here we show that mechanochemistry through isotropic compression is possible by molecularly engineering structures that can translate macroscopic isotropic stress into molecular-level anisotropic strain.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Oxidation of ethane to ethanol by N 2 O in a metal-organic framework with coordinatively unsaturated iron(II) sites

Enzymatic haem and non-haem high-valent iron–oxo species are known to activate strong C–H bonds, yet duplicating this reactivity in a synthetic system remains a formidable challenge. Although instability of the terminal iron–oxo moiety is perhaps the foremost obstacle, steric and electronic factors also limit the activity of previously reported mononuclear iron(IV)–oxo compounds. In particular, although nature's non-haem iron(IV)–oxo compounds possess high-spin S = 2 ground states, this electronic configuration has proved difficult to achieve in a molecular species. These challenges may be mitigated within metal–organic frameworks that feature site-isolated iron centres in a constrained, weak-field ligand environment. Here, we show that the metal–organic framework Fe 2 (dobdc) (dobdc 4- = 2,5-dioxido-1,4-benzenedicarboxylate) and its magnesium-diluted analogue, Fe 0.1 Mg 1.9 (dobdc), are able to activate the C–H bonds of ethane and convert it into ethanol and acetaldehyde using nitrous oxide as the terminal oxidant. Electronic structure calculations indicate that the active oxidant is likely to be a high-spin S = 2 iron(IV)–oxo species.

Xiao, Dianne J.↗

Specific Btk inhibition suppresses B cell- and myeloid cell-mediated arthritis

Bruton's tyrosine kinase (Btk) is a therapeutic target for rheumatoid arthritis, but the cellular and molecular mechanisms by which Btk mediates inflammation are poorly understood. Here we describe the discovery of CGI1746, a small-molecule Btk inhibitor chemotype with a new binding mode that stabilizes an inactive nonphosphorylated enzyme conformation. CGI1746 has exquisite selectivity for Btk and inhibits both auto- and transphosphorylation steps necessary for enzyme activation. Using CGI1746, we demonstrate that Btk regulates inflammatory arthritis by two distinct mechanisms. CGI1746 blocks B cell receptor-dependent B cell proliferation and in prophylactic regimens reduces autoantibody levels in collagen-induced arthritis. In macrophages, Btk inhibition abolishes Fc{gamma}RIII-induced TNF{alpha}, IL-1{beta} and IL-6 production. Accordingly, in myeloid- and Fc{gamma}R-dependent autoantibody-induced arthritis, CGI1746 decreases cytokine levels within joints and ameliorates disease. These results provide new understanding of the function of Btk in both B cell- or myeloid cell-driven disease processes and provide a compelling rationale for targeting Btk in rheumatoid arthritis.

59 BASIC BIOLOGICAL SCIENCES↗

High pressure synthesis of a hexagonal close-packed phase of the high-entropy alloy CrMnFeCoNi

High-entropy alloys, near-equiatomic solid solutions of five or more elements, represent a new strategy for the design of materials with properties superior to those of conventional alloys. However, their phase space remains constrained, with transition metal high-entropy alloys exhibiting only face- or body-centered cubic structures. Here, we report the high-pressure synthesis of a hexagonal close-packed phase of the prototypical high-entropy alloy CrMnFeCoNi. This martensitic transformation begins at 14 GPa and is attributed to suppression of the local magnetic moments, destabilizing the initial fcc structure. Similar to fcc-to-hcp transformations in Al and the noble gases, the transformation is sluggish, occurring over a range of >40 GPa. However, the behaviour of CrMnFeCoNi is unique in that the hcp phase is retained following decompression to ambient pressure, yielding metastable fcc-hcp mixtures. This demonstrates a means of tuning the structures and properties of high-entropy alloys in a manner not achievable by conventional processing techniques.

36 MATERIALS SCIENCE↗

Cesium-mediated electron redistribution and electron-electron interaction in high-pressure metallic CsPbI3

Abstract Electron-phonon coupling was believed to govern the carrier transport in halide perovskites and related phases. Here we demonstrate that electron-electron interaction enhanced by Cs-involved electron redistribution plays a direct and prominent role in the low-temperature electrical transport of compressed CsPbI 3 and renders Fermi liquid (FL)-like behavior. By compressing δ-CsPbI 3 to 80 GPa, an insulator-semimetal-metal transition occurs, concomitant with the completion of a slow structural transition from the one-dimensional Pnma (δ) phase to a three-dimensional Pmn 2 1 (ε) phase. Deviation from FL behavior is observed upon CsPbI 3 entering the metallic ε phase, which progressively evolves into a FL-like state at 186 GPa. First-principles density functional theory calculations reveal that the enhanced electron-electron coupling results from the sudden increase of the 5d state occupation in Cs and I atoms. Our study presents a promising strategy of cationic manipulation for tuning the electronic structure and carrier scattering of halide perovskites at high pressure.

36 MATERIALS SCIENCE↗

Tuning the reactivity of carbon surfaces with oxygen-containing functional groups

Oxygen-containing carbons are promising supports and metal-free catalysts for many reactions. However, distinguishing the role of various oxygen functional groups and quantifying and tuning each functionality is still difficult. Here we investigate the role of Brønsted acidic oxygen-containing functional groups by synthesizing a diverse library of materials. By combining acid-catalyzed elimination probe chemistry, comprehensive surface characterizations, 15N isotopically labeled acetonitrile adsorption coupled with magic-angle spinning nuclear magnetic resonance, machine learning, and density-functional theory calculations, we demonstrate that phenolic is the main acid site in gas-phase chemistries and unexpectedly carboxylic groups are much less acidic than phenolic groups in the graphitized mesoporous carbon due to electron density delocalization induced by the aromatic rings of graphitic carbon. The methodology can identify acidic sites in oxygenated carbon materials in solid acid catalyst-driven chemistry.

Zhou, Jiahua↗

Strain engineered pyrochlore at high pressure

Strain engineering is a promising method for next-generation materials processing techniques. Here, we use mechanical milling and annealing followed by compression in diamond anvil cell to tailor the intrinsic and extrinsic strain in pyrochlore, Dy 2 Ti 2 O 7 and Dy 2 Zr 2 O 7 . Raman spectroscopy, X-ray pair distribution function analysis, and X-ray diffraction were used to characterize atomic order over short-, medium-, and long-range spatial scales, respectively, under ambient conditions. Raman spectroscopy and X-ray diffraction were further employed to interrogate the material in situ at high pressure. High-pressure behavior is found to depend on the species and concentration of defects in the sample at ambient conditions. Overall, we show that defects can be engineered to lower the phase transformation onset pressure by ~50% in the ordered pyrochlore Dy 2 Zr 2 O 7 , and lower the phase transformation completion pressure by ~20% in the disordered pyrochlore Dy 2 Zr 2 O 7 . These improvements are achieved without significantly sacrificing mechanical integrity, as characterized by bulk modulus.

36 MATERIALS SCIENCE↗

Water-Assisted Proton Delivery and Removal in bio-inspired Hydrogen Production Catalysts

Electrocatalysts for H2 production are envisioned to play an important role in renewable energy utilization systems. Nickel-based catalysts featuring pendant amines functioning as proton relays in the second coordination sphere of a metal center have led to catalysts achieving turnover frequencies as high as 107 s-1 for H2 production. The fastest rates are observed when water is present in solution, with rates up to 102 times faster than dry conditions. The focus of this paper is to provide mechanistic insight into the unexpected enhancement due to water. Addition of H2 to [Ni(PR2NR´2)2]2+ was previously shown to give three isomers of a Ni(0) product with two protonated amines, where the N-H can be endo or exo to the Ni. By investigating the deprotonation of two N-protonated Ni(0) intermediates resulting from H2 addition to to [Ni(PR2NR´2)2]2+, we observe an enhancement in the rate of deprotonation for protons positioned on the pendant amine next to the metal (endo) vs. protons that are positioned away from the metal (exo). Computational studies suggest that steric accessibility and desolvation energy of the deprotonating base are responsible for limiting endo deprotonation. The significant reduction in this barrier observed in the presence of water has important implications for disfavoring less productive catalytic pathways and increasing catalytic rates. This research was supported as part of the Center for Molecular Electrocatalysis, an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences. Pacific Northwest National Laboratory is operated by Battelle for the U.S. Department of Energy.

Ho, Ming-Hsun↗

Optimizing conditions for utilization of an H 2 oxidation catalyst with outer coordination sphere functionalities

[Ni(PCy2NArginine2)2]2+ ( CyArg ) or [Ni(PCy2NBenzyl2)2]2+ ( CyBn ) were evaluated for H 2 oxidation as a function of temperature, pressure, and solvent. 70 °C and 100 atm H 2 result in a TOF of 1.1 × 106 s -1 and an overpotential of 240 mV for CyArg in water. In methanol the rates were 280 s -1 for CyArg and 80 s -1 for CyBn , demonstrating the importance of water and the outer coordination sphere ( OCS ).

bio-inspired↗

A fluorescence-electrochemical study of carbon nanodots (CNDs) in bio- and photoelectronic applications and energy gap investigation

Carbon nanodots (CNDs) have attracted significant attention due to their superior solubility, biocompatibility, tunable photoluminescence, and opto-electronic properties. Our work describes a new fluorescence-based spectroelectrochemistry approach to simultaneously study the photoluminescence and wavelength dependent photocurrent of microwave synthesized CNDs. The fluorescence of CNDs shows selective quenching upon a reversible redox couple, ferricyanide/ferrocyanide, reaction during cyclic voltammetry. The CND modified gold slide electrode demonstrates wavelength dependent photocurrent generation during the fluorescence-electrochemical study, suggesting the potential application of CNDs in photoelectronics. UV-Vis absorption and electrochemistry are used to quantify the energy gap of the CNDs, and then to calibrate a Hückel model for CNDs’ electronic energy levels. The Hückel (or tight binding) model treatment of an individual CND as a molecule combines the conjugated π states (C[double bond, length as m-dash]C) with the functional groups (C[double bond, length as m-dash]O, C–O, and COOH) associated with the surface electronic states. This experimental and theoretical investigation of CNDs provides a new perspective on the optoelectronic properties of CNDs and should aid in their development for practical use in biomedicine, chemical sensing, and photoelectric devices.

36 MATERIALS SCIENCE↗

Radiation-induced disorder in compressed lanthanide zirconates

For this study, the effects of swift heavy ion irradiation-induced disordering on the behavior of lanthanide zirconate compounds (Ln 2 Zr 2 O 7 where Ln = Sm, Er, or Nd) at high pressures are investigated. After irradiation with 2.2 GeV 197 Au ions, the initial ordered pyrochlore structure (Fm$\bar{3}$m) transformed to a defect-fluorite structure (Fm$\bar{3}$m) in Sm 2 Zr 2 O 7 and Nd 2 Zr 2 O 7 . For irradiated Er 2 Zr 2 O 7 , which has a defect-fluorite structure, ion irradiation induces local disordering by introducing Frenkel defects despite retention of the initial structure. When subjected to high pressures (>29 GPa) in the absence of irradiation, all of these compounds transform to a cotunnite-like ( Pnma ) phase, followed by sluggish amorphization with further compression. However, if these compounds are irradiated prior to compression, the high pressure cotunnite-like phase is not formed. Rather, they transform directly from their post-irradiation defect-fluorite structure to an amorphous structure upon compression (>25 GPa). Defects and disordering induced by swift heavy ion irradiation alter the transformation pathways by raising the energetic barriers for the transformation to the high pressure cotunnite-like phase, rendering it inaccessible. As a result, the high pressure stability field of the amorphous phase is expanded to lower pressures when irradiation is coupled with compression. The responses of materials in the lanthanide zirconate system to irradiation and compression, both individually and in tandem, are strongly influenced by the specific lanthanide composition, which governs the defect energetics at extreme conditions.

36 MATERIALS SCIENCE↗

Structural characterization of framework–gas interactions in the metal–organic framework Co 2 (dobdc) by in situ single-crystal X-ray diffraction

The crystallographic characterization of framework–guest interactions in metal–organic frameworks allows the location of guest binding sites and provides meaningful information on the nature of these interactions, enabling the correlation of structure with adsorption behavior. Here, techniques developed for in situ single-crystal X-ray diffraction experiments on porous crystals have enabled the direct observation of CO, CH 4 , N 2 , O 2 , Ar, and P 4 adsorption in Co2(dobdc) (dobdc 4– = 2,5-dioxido-1,4-benzenedicarboxylate), a metal–organic framework bearing coordinatively unsaturated cobalt(II) sites. All these molecules exhibit such weak interactions with the high-spin cobalt(II) sites in the framework that no analogous molecular structures exist, demonstrating the utility of metal–organic frameworks as crystalline matrices for the isolation and structural determination of unstable species. Notably, the Co–CH 4 and Co–Ar interactions observed in Co 2 (dobdc) represent, to the best of our knowledge, the first single-crystal structure determination of a metal–CH 4 interaction and the first crystallographically characterized metal–Ar interaction. Analysis of low-pressure gas adsorption isotherms confirms that these gases exhibit mainly physisorptive interactions with the cobalt(II) sites in Co 2 (dobdc), with differential enthalpies of adsorption as weak as –17(1) kJ mol –1 (for Ar). Moreover, the structures of Co 2 (dobdc)·3.8N 2 , Co 2 (dobdc)·5.9O 2 , and Co 2 (dobdc)·2.0Ar reveal the location of secondary (N 2 , O 2 , and Ar) and tertiary (O 2 ) binding sites in Co 2 (dobdc), while high-pressure CO 2 , CO, CH 4 , N 2 , and Ar adsorption isotherms show that these binding sites become more relevant at elevated pressures.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

The structure and unconventional dihydrogen bonding of a pressure-stabilized hydrogen-rich (NH 3 BH 3 )(H 2 ) x (x = 1.5) compound

Combining X-ray diffraction, Raman spectroscopy, and ab initio simulations we characterize an extremely hydrogen-rich phase with the chemical formula (NH 3 BH 3 )(H 2 ) x (x = 1.5). This phase was formed by compressing ammonia borane (AB, NH 3 BH 3 ) in an environment with an excess of molecular hydrogen (H 2 ). This compound can store a total of 26.8 wt% hydrogen, both as molecular hydrogen and chemically bonded hydrogen in AB, making it one of the most hydrogen-rich solids currently known. The new compound possesses a layered AB structure where additional H 2 molecules reside in channels created through the weaving of AB layers. The unconventional dihydrogen bonding network of the new compound is significantly modified from its parent AB phase and contains H•••H contacts between adjacent AB molecules and between AB and H 2 molecules. H–H can be either a proton donor or a proton acceptor that forms new types of dihydrogen bonding with the host AB molecules, which are depicted as H–H•••H–B or H–H•••H–N, respectively. Furthermore, this study not only demonstrates the strategy and the promise of using pressure for new material synthesis, but also unleashes the power of combining experiments and ab initio calculations for elucidating novel structures and unusual bonding configurations in dense low-Z materials.

36 MATERIALS SCIENCE↗

Chicken fat for catalysis: a scaffold is as important for molecular complexes for energy transformations as it is for enzymes in catalytic function

Metalloenzymes are remarkably active, specific, and efficient catalysts.Mimicking the active sites with organometallic complexes based on crystal structures has been a focus for many synthetic chemists. These surrogates have provided significant mechanistic insight into both the molecular complexes as well as the enzymes, however, one of the principle findings has been that just reproducing the active site is not adequate in reproducing the catalytic function. Specifically, the scaffold surrounding the active site plays a critical role in many aspects of catalysis, from positioning reactants optimally to positioning functional groups for reaction to creating the ideal environment for catalysis. Each of these can be controlled with both static positioning as well as small and large dynamics that can activate or control a specific part of the reaction. In this review, we will discuss the effect of organic/peptidic scaffolds, along with medium as an extension of the scaffold, and their varying impacts on catalytic reactivity.

Laureanti, Joseph A.↗