In Situ Monitoring of Non-Thermal Plasma Cleaning of Surfactant Encapsulated Nanoparticles.

Surfactants are widely used in the synthesis of nanoparticles, as they have a remarkable ability to direct their growth to obtain well-defined shapes and sizes. However, their post-synthesis removal is a challenge, and the methods used often result in morphological changes that defeat the purpose of the initial controlled growth. Moreover, after the removal of surfactants, the highly active surfaces of nanomaterials may undergo structural reconstruction by exposure to a different environment. Thus, ex situ characterization after air exposure may not reflect the effect of the cleaning methods. Here, combining X-ray photoelectron spectroscopy, in situ infrared reflection absorption spectroscopy, and environmental transmission electron microscopy measurements with CO probe experiments, we investigated different surfactant-removal methods to produce clean metallic Pt nanoparticles from surfactant-encapsulated ones. It was demonstrated that both ultraviolet-ozone (UV-ozone) treatment and room temperature O2 plasma treatment led to the formation of Pt oxides on the surface after the removal of the surfactant. On the other hand, when H2 was used for plasma treatment, both the Pt0 oxidation state and nanoparticle size distribution were preserved. In addition, H2 plasma treatment can reduce Pt oxides after O2-based treatments, resulting in metallic nanoparticles with clean surfaces. These findings provide a better understanding of the various options for surfactant removal from metal nanoparticles and point toward non-thermal plasmas as the best route if the integrity of the nanoparticle needs to be preserved.

Role of H2O in Catalytic Conversion of C1 Molecules.

Due to their role in controlling global climate change, the selective conversion of C1 molecules such as CH4, CO, and CO2 has attracted widespread attention. Typically, H2O competes with the reactant molecules to adsorb on the active sites and therefore inhibits the reaction or causes catalyst deactivation. However, H2O can also participate in the catalytic conversion of C1 molecules as a reactant or a promoter. Herein, we provide a perspective on recent progress in the mechanistic studies of H2O-mediated conversion of C1 molecules. We aim to provide an in-depth and systematic understanding of H2O as a promoter, a proton-transfer agent, an oxidant, a direct source of hydrogen or oxygen, and its influence on the catalytic activity, selectivity, and stability. We also summarize strategies for modifying catalysts or catalytic microenvironments by chemical or physical means to optimize the positive effects and minimize the negative effects of H2O on the reactions of C1 molecules. Finally, we discuss challenges and opportunities in catalyst design, characterization techniques, and theoretical modeling of the H2O-mediated catalytic conversion of C1 molecules.

The Natural Products Discovery Center: Release of the First 8490 Sequenced Strains for Exploring Actinobacteria Biosynthetic Diversity.

Actinobacteria, the bacterial phylum most renowned for natural product discovery, has been established as a valuable source for drug discovery and biotechnology but is underrepresented within accessible genome and strain collections. Herein, we introduce the Natural Products Discovery Center (NPDC), featuring 122,449 strains assembled over eight decades, the genomes of the first 8490 NPDC strains (7142 Actinobacteria), and the online NPDC Portal making both strains and genomes publicly available. A comparative survey of RefSeq and NPDC Actinobacteria highlights the taxonomic and biosynthetic diversity within the NPDC collection, including three new genera, hundreds of new species, and ~7000 new gene cluster families. Selected examples demonstrate how the NPDC Portal's strain metadata, genomes, and biosynthetic gene clusters can be leveraged using genome mining approaches. Our findings underscore the ongoing significance of Actinobacteria in natural product discovery, and the NPDC serves as an unparalleled resource for both Actinobacteria strains and genomes.

Ultrathin Magnesium-Based Coating as an Efficient Oxygen Barrier for Superconducting Circuit Materials.

Scaling up superconducting quantum circuits based on transmon qubits necessitates substantial enhancements in qubit coherence time. Over recent years, tantalum (Ta) has emerged as a promising candidate for transmon qubits, surpassing conventional counterparts in terms of coherence time. However, amorphous surface Ta oxide layer may introduce dielectric loss, ultimately placing a limit on the coherence time. In this study, a novel approach for suppressing the formation of tantalum oxide using an ultrathin magnesium (Mg) capping layer is presented. Synchrotron-based X-ray photoelectron spectroscopy studies demonstrate that oxide is confined to an extremely thin region directly beneath the Mg/Ta interface. Additionally, it is demonstrated that the superconducting properties of thin Ta films are improved following the Mg capping, exhibiting sharper and higher-temperature transitions to superconductive and magnetically ordered states. Moreover, an atomic-scale mechanistic understanding of the role of the capping layer in protecting Ta from oxidation is established based on computational modeling. This work provides valuable insights into the formation mechanism and functionality of surface tantalum oxide, as well as a new materials design principle with the potential to reduce dielectric loss in superconducting quantum materials. Ultimately, the findings pave the way for the realization of large-scale, high-performance quantum computing systems.

Cofactorless oxygenases guide anthraquinone-fused enediyne biosynthesis.

The anthraquinone-fused enediynes (AFEs) combine an anthraquinone moiety and a ten-membered enediyne core capable of generating a cytotoxic diradical species. AFE cyclization is triggered by opening the F-ring epoxide, which is also the site of the most structural diversity. Previous studies of tiancimycin A, a heavily modified AFE, have revealed a cryptic aldehyde blocking installation of the epoxide, and no unassigned oxidases could be predicted within the tnm biosynthetic gene cluster. Here we identify two consecutively acting cofactorless oxygenases derived from methyltransferase and α/ß-hydrolase protein folds, TnmJ and TnmK2, respectively, that are responsible for F-ring tailoring in tiancimycin biosynthesis by comparative genomics. Further biochemical and structural characterizations reveal that the electron-rich AFE anthraquinone moiety assists in catalyzing deformylation, epoxidation and oxidative ring cleavage without exogenous cofactors. These enzymes therefore fill important knowledge gaps for the biosynthesis of this class of molecules and the underappreciated family of cofactorless oxygenases.

Functional Characterization of Cytochrome P450 Hydroxylase YpmL in Yangpumicin A Biosynthesis and Its Application for Anthraquinone-Fused Enediyne Structural Diversification.

Comparative analyses of four anthraquinone-fused enediyne biosynthetic gene clusters (BGCs) identified YpmL as a cytochrome P450 enzyme unique to the yangpumicin (YPM) BGC. In vitro characterization of YpmL established it as a hydroxylase, catalyzing C-6 hydroxylation in YPM A biosynthesis. In vivo application of YpmL enabled engineered production of four new tiancimycin analogues (14-17). Evaluation of their cytotoxicity against selected human cancer cell lines shed new insights into the enediyne structure-activity relationship.

Structural and biochemical studies of an iterative ribosomal peptide macrocyclase.

Microviridins, tricyclic peptide natural products originally isolated from cyanobacteria, function as inhibitors of diverse serine-type proteases. Here we report the structure and biochemical characterization of AMdnB, a unique iterative macrocyclase involved in a microviridin biosynthetic pathway from Anabaena sp. PCC 7120. The ATP-dependent cyclase, along with the homologous AMdnC, introduce up to nine macrocyclizations on three distinct core regions of a precursor peptide, AMdnA. The results presented here provide structural and mechanistic insight into the iterative chemistry of AMdnB. In vitro AMdnB-catalyzed cyclization reactions demonstrate the synthesis of the two predicted tricyclic products from a multi-core precursor peptide substrate, consistent with a distributive mode of catalysis. The X-ray structure of AMdnB shows a structural motif common to ATP-grasp cyclases involved in RiPPs biosynthesis. Additionally, comparison with the noniterative MdnB allows insight into the structural basis for the iterative chemistry. Overall, the presented results provide insight into the general mechanism of iterative enzymes in ribosomally synthesized and post-translationally modified peptide biosynthetic pathways.

Structure-Based Engineering of Peptide Macrocyclases for the Chemoenzymatic Synthesis of Microviridins.

Microviridins are cyanobacterial tricyclic depsipeptides with unique ring architectures and function as serine protease inhibitors. In this study, we explore two strategies to probe the structure and mechanism of macrocyclases involved in microviridin biosynthesis. The results both provide approaches for in vitro chemoenzymatic synthesis and insight into the molecular interactions and function of the biosynthetic enzymes. The first strategy involves generating constitutively activated macrocyclases whereby the leader portion of the substrate peptide is covalently attached to the ATP-grasp ligases to examine leader peptide/enzyme interactions. The second strategy uses a structure-based design to create disulfide cross-linked peptide/enzyme complexes. Together, the strategies provide constitutively active enzymes and tools to study the catalysis of the macrocyclizations on synthetic core peptides.

Energetic Cost for Being "Redox-Site-Rich" in Pseudocapacitive Energy Storage with Nickel-Aluminum Layered Double Hydroxide Materials.

Defining the energetic landscape of pseudocapacitive materials such as transition metal layered double hydroxides (LDHs) upon redox-site enrichment is essential to harnessing their power for effective energy storage. Here, coupling acid solution calorimetry, in situ XRD, and in situ DRIFTS, we demonstrate that as the Ni/Al ratio increases, both as-made (hydrated) and dehydrated NiAl-LDH samples are less stable as evidenced by their enthalpies of formation. Moreover, the higher specific capacity at an intermediate Ni/Al ratio of 3 is enabled by effective water-LDH interactions, which energetically stabilize the excessive near-surface Ni redox sites, solvate intercalated carbonate ions, and fill the expanded vdW gap, paying for the "energetic cost" of being "redox-site-rich". Thus, from a thermodynamic perspective, engineering molecule/solid-LDH interactions on the nanoscale with confined guest species other than water, which energetically impose stronger stabilization, may help us to achieve their specific capacitance potential.

Synthesis of α,ß- and ß-Unsaturated Acids and Hydroxy Acids by Tandem Oxidation, Epoxidation, and Hydrolysis/Hydrogenation of Bioethanol Derivatives.

We report a reaction platform for the synthesis of three different high-value specialty chemical building blocks starting from bio-ethanol, which might have an important impact in the implementation of biorefineries. First, oxidative dehydrogenation of ethanol to acetaldehyde generates an aldehyde-containing stream active for the production of C4 aldehydes via base-catalyzed aldol-condensation. Then, the resulting C4 adduct is selectively converted into crotonic acid via catalytic aerobic oxidation (62 % yield). Using a sequential epoxidation and hydrogenation of crotonic acid leads to 29 % yield of ß-hydroxy acid (3-hydroxybutanoic acid). By controlling the pH of the reaction media, it is possible to hydrolyze the oxirane moiety leading to 21 % yield of α,ß-dihydroxy acid (2,3-dihydroxybutanoic acid). Crotonic acid, 3-hydroxybutanoic acid, and 2,3-dihydroxybutanoic acid are archetypal specialty chemicals used in the synthesis of polyvinyl-co-unsaturated acids resins, pharmaceutics, and bio-degradable/ -compatible polymers, respectively.

High-Temperature Grafting Silylation for Minimizing Leaching of Acid Functionality from Hydrophobic Mesoporous Silicas Used as Catalysts in the Liquid Phase.

Ordered-hexagonal silica materials, such as Mobil crystalline material-41 and Santa Barbara amorphous-15, have important applications in heterogeneous catalysis and biomass conversion due to their chemical stability and mesoporous structure. Low-temperature grafting (LG) is one of the most common functionalization methods used to modify the acidity/basicity or hydrophobicity/hydrophilicity of the surface. However, the materials prepared by this method are prone to leaching of functional groups into the reaction medium. The exact nature of the leaching phenomenon has not been fully addressed in the literature. In this contribution, we have investigated this process at the molecular level by combining well-controlled reaction experiments and several characterization techniques (Fourier transform infrared, 1H-29Si cross-polarization magic-angle spinning NMR, X-ray diffraction, thermogravimetric analysis, and N2 adsorption-desorption). We have found that leaching is originated by the presence of terminal surface silanols, which render the catalysts susceptible to the attack of water and polar compounds. Hence, instead of simple detaching of functional groups, leaching can be better described as a partial dissolution of the surface layers of the silica, which of course also removes the functional groups during this process. Therefore, an effective strategy to minimize leaching is to reduce the density of free silanols via full functionalization of the surface. We propose a novel silylation method, high-temperature grafting, which allows the grafting process to be conducted at high temperatures (180 °C) under solvent-free conditions. By this method, a more complete silylation of surface silanols can be obtained. Consequently, the samples prepared by this high-temperature grafting method show to be highly stable during acid-catalyzed alkylation reaction, conducted under severe conditions (high temperature and in the presence of polar solvents).

Self-Templated Synthesis of Porous Ni(OH)2 Nanocube and Its High Electrochemical Performance for Supercapacitor.

Porous Ni(OH)2 nanocubes were successfully fabricated by a simple self-sacrificial-template protocol using Ni-Co Prussian blue analogue (PBA) as precursor. When treated with NaOH, the simultaneous corrosion of Ni-Co PBA precursor and formation of amorphous Ni(OH)2 resulted in porous Ni(OH)2 nanocubes with uniform size of about 100 nm. Due to the large specific surface area and unique regular porous structure, the as-prepared materials showed large specific capacitance, relatively stable rate capability and long cycle stability when used as electrode materials for supercapacitors. With the voltage between 0.00 and 0.45 V versus Ag/AgCl, the specific capacitance can achieve 1842 F/g at a current density of 1 A/g.

Cytotoxic protein from the mushroom Coprinus comatus possesses a unique mode for glycan binding and specificity.

Glycans possess significant chemical diversity; glycan binding proteins (GBPs) recognize specific glycans to translate their structures to functions in various physiological and pathological processes. Therefore, the discovery and characterization of novel GBPs and characterization of glycan-GBP interactions are significant to provide potential targets for therapeutic intervention of many diseases. Here, we report the biochemical, functional, and structural characterization of a 130-amino-acid protein, Y3, from the mushroom Coprinus comatus Biochemical studies of recombinant Y3 from a yeast expression system demonstrated the protein is a unique GBP. Additionally, we show that Y3 exhibits selective and potent cytotoxicity toward human T-cell leukemia Jurkat cells compared with a panel of cancer cell lines via inducing caspase-dependent apoptosis. Screening of a glycan array demonstrated GalNAcß1-4(Fucα1-3)GlcNAc (LDNF) as a specific Y3-binding ligand. To provide a structural basis for function, the crystal structure was solved to a resolution of 1.2 Å, revealing a single-domain αßα-sandwich motif. Two monomers were dimerized to form a large 10-stranded, antiparallel ß-sheet flanked by α-helices on each side, representing a unique oligomerization mode among GBPs. A large glycan binding pocket extends into the dimeric interface, and docking of LDNF identified key residues for glycan interactions. Disruption of residues predicted to be involved in LDNF/Y3 interactions resulted in the significant loss of binding to Jurkat T-cells and severely impaired their cytotoxicity. Collectively, these results demonstrate Y3 to be a GBP with selective cytotoxicity toward human T-cell leukemia cells and indicate its potential use in cancer diagnosis and treatment.

Highly Efficiently Delaminated Single-Layered MXene Nanosheets with Large Lateral Size.

Single layered Ti3C2(OH)2 nanosheets have been successfully fabricated by etching its Ti3AlC2 precursor with KOH in the presence of a small amount of water. The OH group replaced the Al layer within the Ti3AlC2 structure during etching, and Ti3C2(OH)2 nanosheets could be easily and efficiently achieved through a simple washing process. The delaminated single-layered nanosheets are clearly revealed by atomic force microscopy to be several micrometers in lateral size. Interestingly, the exfoliated Ti3C2(OH)2 nanosheets could be restacked to form a new layer-structured material after drying. When redispersing this restacked Ti3C2(OH)2 materials in water again, it could be re-delaminated easily only after shaking for several hours. The easy delamination and restacking properties, coupled with intrinsic metallic conductivity and hydrophilicity, make it an ideal two-dimensional building block for fabricating a wide variety of functional materials.

A strictly monofunctional bacterial hydroxymethylpyrimidine phosphate kinase precludes damaging errors in thiamin biosynthesis.

The canonical kinase (ThiD) that converts the thiamin biosynthesis intermediate hydroxymethylpyrimidine (HMP) monophosphate to the diphosphate can also very efficiently convert free HMP to the monophosphate in prokaryotes, plants, and fungi. This HMP kinase activity enables salvage of HMP, but it is not substrate-specific and so allows toxic HMP analogs and damage products to infiltrate the thiamin biosynthesis pathway. Comparative analysis of bacterial genomes uncovered a gene, thiD2 , that is often fused to the thiamin synthesis gene thiE and could potentially encode a replacement for ThiD. Standalone ThiD2 proteins and ThiD2 fusion domains are small (~130-residues) and do not belong to any previously known protein family. Genetic and biochemical analyses showed that representative standalone and fused ThiD2 proteins catalyze phosphorylation of HMP monophosphate, but not of HMP or its toxic analogs and damage products such as bacimethrin and 5-(hydroxymethyl)-2-methylpyrimidin-4-ol. As strictly monofunctional HMP monophosphate kinases, ThiD2 proteins eliminate a potentially fatal vulnerability of canonical ThiD, at the cost of the ability to reclaim HMP formed by thiamin turnover.

Alkali-assisted mild aqueous exfoliation for single-layered and structure-preserved graphitic carbon nitride nanosheets.

Single-layered g-C3N4 nanosheets have been fabricated by delaminating directly its bulk counterpart in an alkaline solution. According to the theoretical modeling, the interaction of OH- with terminal NH2 or bridged NH group of the triazine units within bulk g-C3N4 crystal structure could result in decreased bonding energy between layers and promote the total delamination. The resulting g-C3N4 nanosheets colloid has a relatively high concentration (12g/L) compared with the traditional ultrasonic assistant exfoliation method. The delaminated nanosheets are revealed by atomic force microscopy to show a lateral size of a hundred nanometers and a thickness of about 0.4nm, which provides a direct evidence for the total exfoliation of g-C3N4 crystals into their single sheets. More importantly, the X-ray diffraction measurement confirms that the g-C3N4 nanosheets could be re-assembled with well-preserved original crystal structure. The exfoliation mechanism was also confirmed by the DFT calculation.

Structural basis for precursor protein-directed ribosomal peptide macrocyclization.

Macrocyclization is a common feature of natural product biosynthetic pathways including the diverse family of ribosomal peptides. Microviridins are architecturally complex cyanobacterial ribosomal peptides that target proteases with potent reversible inhibition. The product structure is constructed via three macrocyclizations catalyzed sequentially by two members of the ATP-grasp family, a unique strategy for ribosomal peptide macrocyclization. Here we describe in detail the structural basis for the enzyme-catalyzed macrocyclizations in the microviridin J pathway of Microcystis aeruginosa. The macrocyclases MdnC and MdnB interact with a conserved α-helix of the precursor peptide using a novel precursor-peptide recognition mechanism. The results provide insight into the unique protein-protein interactions that are key to the chemistry, suggest an origin for the natural combinatorial synthesis of microviridin peptides, and provide a framework for future engineering efforts to generate designed compounds.

Crystal structure of the homocysteine methyltransferase MmuM from Escherichia coli.

Homocysteine S-methyltransferases (HMTs, EC 2.1.1.0) catalyse the conversion of homocysteine to methionine using S-methylmethionine or S-adenosylmethionine as the methyl donor. HMTs play an important role in methionine biosynthesis and are widely distributed among micro-organisms, plants and animals. Additionally, HMTs play a role in metabolite repair of S-adenosylmethionine by removing an inactive diastereomer from the pool. The mmuM gene product from Escherichia coli is an archetypal HMT family protein and contains a predicted zinc-binding motif in the enzyme active site. In the present study, we demonstrate X-ray structures for MmuM in oxidized, apo and metallated forms, representing the first such structures for any member of the HMT family. The structures reveal a metal/substrate-binding pocket distinct from those in related enzymes. The presented structure analysis and modelling of co-substrate interactions provide valuable insight into the function of MmuM in both methionine biosynthesis and cofactor repair.

Controlled one-step synthesis of Pt decorated octahedral Fe3O4 and its excellent catalytic performance for CO oxidation.

A facile one-step co-precipitation method has been applied for the synthesis of a Pt decorated octahedral Fe3O4 catalyst. The simple addition of a Pt(4+) and Fe(2+) mixture into a KOH solution leads to the simultaneous formation of an octahedral Fe3O4 and in situ reduction of Pt(4+). HAADF-STEM analysis demonstrates the good dispersion of the Pt species on the Fe3O4 (111) plane, and the resulting material exhibits excellent catalytic activity for CO oxidation under moisture conditions. The inevitably existing moisture contributes to the formation of reaction intermediate [COOH] and hence promotes the catalytic activity, which has been proved through in situ DRIFTS analysis.

One-pot synthesis of meso-structured Pd-CeOx catalyst for efficient low-temperature CO oxidation under ambient conditions.

A facile one-pot co-precipitation approach was applied to fabricate a meso-structured Pd-CeOx composite for low temperature CO oxidation. The as-prepared material had a much higher specific area and highly dispersed noble metal species, and thus showed excellent catalytic activity and stability for CO oxidation, especially under ambient conditions. Complete CO conversion could be achieved at as low as 25 °C for 5.9 wt% Pd doped catalyst, when 3.0 vol% H2O was introduced into the feed gas. The reaction mechanism on such a catalyst has been proposed through in situ DRIFTS and kinetic analysis.