Exploration of whole genome amplification generated chimeric sequences in long-read sequencing data.

MOTIVATION: Multiple displacement amplification (MDA) has become the most commonly used method of whole genome amplification, generating a vast amount of DNA with higher molecular weight and greater genome coverage. Coupling with long-read sequencing, it is possible to sequence the amplicons of over 20 kb in length. However, the formation of chimeric sequences (chimeras, expressed as structural errors in sequencing data) in MDA seriously interferes with the bioinformatics analysis but its influence on long-read sequencing data is unknown. RESULTS: We sequenced the phi29 DNA polymerase-mediated MDA amplicons on the PacBio platform and analyzed chimeras within the generated data. The 3rd-ChimeraMiner has been constructed as a pipeline for recognizing and restoring chimeras into the original structures in long-read sequencing data, improving the efficiency of using TGS data. Five long-read datasets and one high-fidelity long-read dataset with various amplification folds were analyzed. The result reveals that the mis-priming events in amplification are more frequently occurring than widely perceived, and the propor tion gradually accumulates from 42% to over 78% as the amplification continues. In total, 99.92% of recognized chimeric sequences were demonstrated to be artifacts, whose structures were wrongly formed in MDA instead of existing in original genomes. By restoring chimeras to their original structures, the vast majority of supplementary alignments that introduce false-positive structural variants are recycled, removing 97% of inversions on average and contributing to the analysis of structural variation in MDA-amplified samples. The impact of chimeras in long-read sequencing data analysis should be emphasized, and the 3rd-ChimeraMiner can help to quantify and reduce the influence of chimeras. AVAILABILITY AND IMPLEMENTATION: The 3rd-ChimeraMiner is available on GitHub, https://github.com/dulunar/3rdChimeraMiner.

Wafer Scale Gallium Nitride Integrated Electrode Toward Robust High Temperature Energy Storage.

Gallium Nitride (GaN), as the representative of wide bandgap semiconductors, has great prospects in accomplishing rapid charge delivery under high-temperature environments thanks to excellent structural stability and electron mobility. However, there is still a gap in wafer-scale GaN single-crystal integrated electrodes applied in the energy storage field. Herein, Si-doped GaN nanochannel with gallium oxynitride (GaON) layer on a centimeter scale (denoted by GaN NC) is reported. The Si atoms modulate electronic redistribution to improve conductivity and drive nanochannel formation. Apart from that, the distinctive nanochannel configuration with a GaON layer provides adequate active sites and extraordinary structural stability. The GaN-based supercapacitors are assembled and deliver outstanding charge storage capabilities at 140 °C. Surprisingly, 90% retention is maintained after 50 000 cycles. This study opens the pathway toward wafer-scale GaN single-crystal integrated electrodes with self-powered characteristics that are compatible with various (opto)-electronic devices.

Unveiling the Structural Origins of Dynamic Diversity in Pd-Based Metallic Glasses.

The ß-relaxation is one of the major dynamic behaviors in metallic glasses (MGs) and exhibits diverse features. Despite decades of efforts, the understanding of its structural origin and contribution to the overall dynamics of MG systems is still unclear. Here two palladium-based Pd─Cu─P and Pd─Ni─P MGs are reported with distinct different ß-relaxation behaviors and reveal the structural origins for the difference using the advanced X-ray photon correlation spectroscopy and absorption fine structure techniques together with the first-principles calculations. The pronounced ß-relaxation and fast atomic dynamics in the Pd─Cu─P MG mainly come from the strong mobility of Cu atoms and their locally favored structures. In contrast, the motion of Ni atoms is constrained by P atoms in the Pd─Ni─P MG, leading to the weakened ß-relaxation peak and sluggish dynamics. The correlation of atomic dynamics with microscopic structures provides a way to understand the structural origins of different dynamic behaviors as well as the nature of aging in disordered materials.

Selective Activation of Lattice Oxygen Site Through Coordination Engineering to Boost the Activity and Stability of Oxygen Evolution Reaction.

Although Ru-based materials are among the outstanding catalysts for the oxygen evolution reaction (OER), the instability issue still haunts them and impedes the widespread application. The instability of Ru-based OER catalysts is generally ascribed to the formation of soluble species through the over-oxidation of Ru and structural decomposition caused by involvement of lattice oxygen. Herein, an effective strategy of selectively activating the lattice oxygen around Ru site is proposed to improve the OER activity and stability. Our synthesized spinel-type electrocatalyst of Ru and Zn co-doped Co3O4 showed an ultralow overpotential of 172 mV at 10 mA cm-2 and a long-term stability reaching to 100 hours at 10 mA cm-2 for alkaline OER. The experimental results and theoretical simulations demonstrated that the lattice oxygen site jointly connected with the octahedral Ru and tetrahedral Zn atoms became more active than other oxygen sites near Ru atom, which further lowered the reaction energy barriers and avoided generating excessive oxygen vacancies to enhance the structural stability of Ru sites. The findings hope to provide a new perspective to improve the catalytic activity of Ru-incorporated OER catalysts and the stability of lattice-oxygen-mediated mechanism.

Modulating Charges of Dual Sites in Multivariate Metal-Organic Frameworks for Boosting Selective Aerobic Epoxidation of Alkenes.

Selective aerobic epoxidation of alkenes without any additives is of great industrial importance but still challenging because the competitive side reactions including C═C bond cleavage and isomerization are difficult to avoid. Here, we show fabricating Cu(I) single sites in pristine multivariate metal-organic frameworks (known as CuCo-MOF-74) via partial reduction of Cu(II) to Cu(I) ions during solvothermal reaction. Impressively, CuCo-MOF-74 is characteristic with single Cu(I), Cu(II), and Co(II) sites, and they exhibit the substantially enhanced selectivity of styrene oxide up to 87.6% using air as an oxidant at almost complete conversion of styrene, ∼25.8% selectivity increased over Co-MOF-74, as well as good catalytic stability. Contrast experiments and theoretical calculation indicate that Cu(I) sites contribute to the substantially enhanced selectivity of epoxides catalyzed by Co(II) sites. The adsorption of two O2 molecules on dual Co(II) and Cu(I) sites is favorable, and the projected density of state of the Co-3d orbital is closer to the Fermi level by modulating with Cu(I) sites for promoting the activation of O2 compared with dual-site Cu(II) and Co(II) and Co(II) and Co(II), thus contributing to the epoxidation of the C═C bond. When other kinds of alkenes are used as substrates, the excellent selectivity of various epoxides is also achieved over CuCo-MOF-74. We also prove the universality of fabricating Cu(I) sites in other MOF-74 with various divalent metal nodes.

Selective Hydrodeoxygenation of Aromatics to Cyclohexanols over Ru Single Atoms Supported on CeO2.

Cyclohexanols are widely used chemicals, which are mainly produced by oxidation of fossil feedstocks. Selective hydrodeoxygenation of lignin derivatives has great potential for producing these chemicals but is challenging to obtain high yields. Here, we report that CeO2-supported Ru single-atom catalysts (SACs) enabled the hydrogenation of the benzene ring and catalyzed etheric C-O(R) bond cleavage without changing the C-O(H) bond, which could afford 99.9% yields of cyclohexanols. As far as we know, this is the first to report that SACs catalyze hydrogenation of the aromatic ring. The reaction mechanism was studied by control experiments and density functional theory calculations. In the catalysts, the Ru-O-Ce sites were formed and one Ru atom was coordinated with about four O atoms. These catalytic sites could realize both the hydrogenation and deoxygenation reactions efficiently, and thus desired cyclohexanols were generated. This work pioneers the single-atom catalysis in aromatic transformation and provides a novel route for synthesis of cyclohexanols.

Electronic Configurations and the Effect of Peripheral Substituents of (Nitrosyl)iron Corroles.

There have been debates on the electronic configurations of (nitrosyl)iron corroles for decades. In this work, pentacoordinate [Fe(TPC)(NO)], [Fe(TTC)(NO)], and [Fe(TpFC)(NO)] with different para-substituted phenyl groups (TPC, TTC, and TpFC = tris(phenyl, 4-tolyl, or 4-fluorophenyl)corrole, respectively) have been isolated and investigated by various techniques including single-crystal X-ray diffraction, UV-vis spectroscopy, cyclic voltammetry, Fourier transform infrared, NMR, and absorption fine structure spectroscopy. Multitemperature and high-magnetic-field (3, 6, and 9 T) Mössbauer spectroscopy was also applied on all three complexes, which determined the S = 0 diamagnetic states, consistent with the magnetic susceptibility and electron paramagnetic resonance measurements. Density functional theory predictions by different functionals were compared, and the new calculation strategy, which gave remarkable agreement of the experimental Mössbauer parameters (ΔEQ and δ), allowed further assignment on the electronic configuration of {FeNO}6-(corrole3-) with antiferromagnetically coupled (S = 1/2, FeIII) and (S = 1/2, NO). Correlated sequences between the electronic donating/withdrawing capability of para substituents and the reduction/oxidation potentials, metal out-of-plane displacements (Δ4 and Δ23), and Mössbauer parameters (Vzz and ΔEQ) were also established, which suggests the strong effects of peripheral substituents.

Two-Dimensional-on-Three-Dimensional Metal-Organic Frameworks for Photocatalytic H2 Production.

A MOF-on-MOF heterostructure is attractive in material science because of its potential combined effects in catalysis. However, precisely controlling the growth pattern at the metal-organic framework (MOF) nucleation stage to manipulate the metallic composition and structure dimensionality remain a challenge. Herein, we introduce a polyvinylpyrrolidone-assist kinetic-control strategy to achieve the "anti-epitaxial growth" pattern of a foreign MOF nucleus on the (111) facets of UiO-66-NH2 octahedron seeds, and construct diverse two-dimensional-on-three-dimensional (2D-on-3D) MOF heterostructures (2D-on-3D Cu, Zn, Cd, Co, and Ni). Notably, the 2D-on-3D Cu exhibits a unique "dimensionality-hybrid" effect in photocatalysis which led to a significant photoactivity enhancement over those of the traditional "dimensionality-identical" 2D, 3D and 3D-on-3D MOF structures.

Dynamic Restructuring of Coordinatively Unsaturated Copper Paddle Wheel Clusters to Boost Electrochemical CO2 Reduction to Hydrocarbons.

The electrochemical reduction of CO2 to hydrocarbons involves a multistep proton-coupled electron transfer (PCET) reaction. Second coordination sphere engineering is reported to be effective in the PCET process; however, little is known about the actual catalytic active sites under realistic operating conditions. We have designed a defect-containing metal-organic framework, HKUST-1, through a facile "atomized trimesic acid" strategy, in which Cu atoms are modified by unsaturated carboxylate ligands, producing coordinatively unsaturated Cu paddle wheel (CU-CPW) clusters. We investigate the dynamic behavior of the CU-CPW during electrochemical reconstruction through the comprehensive analysis of in situ characterization results. It is demonstrated that Cu2 (HCOO)3 is maintained after electrochemical reconstruction and that is behaves as an active site. Mechanistic studies reveal that CU-CPW accelerates the proton-coupled multi-electron transfer (PCMET) reaction, resulting in a deep CO2 reduction reaction.

Single-Atom Doping and High-Valence State for Synergistic Enhancement of NiO Electrocatalytic Water Oxidation.

The NiO-based electrocatalytic oxygen evolution reaction (OER) of water splitting is recognized as a promising approach to produce clean H2 fuel. However, the OER performance is still low, and especially, the overpotential is larger than 200 mV at the current density of 10 mA cm-2 . Herein, an Ir@IrNiO sample is prepared with single-atom (SA) Ir4+ doping and surface metallic Ir nanoparticles loaded onto the NiO. Owing to the bonding of the loaded Ir with surface-exposed Ni2+ , the nearby Ni atoms exist in the +3 valence state, that is, the surface-loaded Ir particles behave like a stabilizer for the Ni3+ sites. Under the synergistic effect of SA Ir4+ and high-valance-state Ni3+ , the Ir@IrNiO nanostructure effectively reduces the overpotential to 195 mV at a current density of 10 mA cm-2 . Moreover, it gives an Ir-content-normalized current density of 0.0457 A mgIr -1 , 72.1 times higher than that of the best commercialized IrO2 (6.33 × 10-4 A mgIr -1 ), under the condition of 1.5 V versus reversible hydrogen electrode. Operando Raman and X-ray absorption fine-structure (XAFS) measurements reveal that there are more surface-active species of Ni3+ , which adsorb and activate water molecules to form Ni3+ -*OH at low voltage, the intermediate of Ni4+ -•O is then formed at a relatively high bias voltage, and then the •O is transferred to the SA Ir4+ sites to generate Ir4+ -O-O with OH at increased voltage. This work can help design more SA-based highly active OER materials.

Fe-Ni Alloy Nanoclusters Anchored on Carbon Aerogels as High-Efficiency Oxygen Electrocatalysts in Rechargeable Zn-Air Batteries.

In this work, Fe-Ni alloy nanoclusters (Fe-Ni ANCs) anchored on N, S co-doped carbon aerogel (Fe-Ni ANC@NSCA catalysts) are successfully prepared by the optimal pyrolysis of polyaniline (PANI) aerogels derived from the freeze-drying of PANI hydrogel obtained by the polymerization of aniline monomers in the co-presence of tannic acid (TA), Fe3+ , and Ni2+ ions. In addition, the optimal molar ratio of the TA, Fe3+ , and Ni2+ ions for synthesis of Fe-Ni ANC@NSCA catalysts are 1:2:5, which can guarantee the formation of carbon aerogel composed of quasi-2D porous carbon sheets and the formation of high-density Fe-Ni ANCs with an ultrasmall size between 2 to 2.8 nm. These Fe-Ni ANCs consisting of N4 -Fe-O-Ni-N4 moiety are proposed as a new type of active species for the first time, to the best of the authors' knowledge. Thanks to their unique features, the Fe-Ni ANC@NSCA catalysts show excellent performance in oxygen reduction reaction with a half-wave potential (E1/2 ) of 0.891 V and oxygen evolution reaction (260 mV @ 10 mA cm-2 ) in alkaline media as bifunctional catalysts, which are better than the state-of-the-art commercial Pt/C catalysts and RuO2 catalysts. Moreover, Zn-air battery assembled with the Fe-Ni ANC@NSCA catalysts also shows a remarkable performance and exceptionally high stability over 500 h at 5 mA cm-2 .

P3/O3 Integrated Layered Oxide as High-Power and Long-Life Cathode toward Na-Ion Batteries.

Low-cost and stable sodium-layered oxides (such as P2- and O3-phases) are suggested as highly promising cathode materials for Na-ion batteries (NIBs). Biphasic hybridization, mainly involving P2/O3 and P2/P3 biphases, is typically used to boost their electrochemical performances. Herein, a P3/O3 intergrown layered oxide (Na2/3 Ni1/3 Mn1/3 Ti1/3 O2 ) as high-rate and long-life cathode for NIBs via tuning the amounts of Ti substitution in Na2/3 Ni1/3 Mn2/3- x Tix O2 (x = 0, 1/6, 1/3, 2/3) is demonstrated. The X-ray diffraction (XRD) Rietveld refinement and aberration-corrected scanning transmission electron microscopy show the co-existence of P3 and O3 phases, and density functional theory calculation corroborates the appearance of the anomalous O3 phase at the Ti substitution amount of 1/3. The P3/O3 biphasic cathode delivers an unexpected rate capability (≈88.7% of the initial capacity at a high rate of 5 C) and cycling stability (≈68.7% capacity retention after 2000 cycles at 1 C), superior to those of the sing phases P3-Na2/3 Ni1/3 Mn2/3 O2 , P3-Na2/3 Ni1/3 Mn1/2 Ti1/6 O2 , and O3-Na2/3 Ni1/3 Ti2/3 O2 . The highly reversible structural evolution of the P3/O3 integrated cathode observed by ex situ XRD, ex situ X-ray absorption spectra, and the rapid Na+ diffusion kinetics, underpin the enhancement. These results show the important role of P3/O3 biphasic hybridization in designing and engineering layered oxide cathodes for NIBs.

Fe-O Clusters Anchored on Nodes of Metal-Organic Frameworks for Direct Methane Oxidation.

Direct methane oxidation into value-added organic oxygenates with high productivity under mild condition remains a great challenge. We show Fe-O clusters on nodes of metal-organic frameworks (MOFs) with tunable electronic state for direct methane oxidation into C1 organic oxygenates at 50 °C. The Fe-O clusters are grafted onto inorganic Zr6 nodes of UiO-66, while the organic terephthalic acid (H2 BDC) ligands of UiO-66 are partially substituted with monocarboxylic modulators of acetic acid (AA) or trifluoroacetic acid (TFA). Experiments and theoretical calculation disclose that the TFA group coordinated with Zr6 node of UiO-66 enhances the oxidation state of adjacent Fe-O cluster due to its electron-withdrawing ability, promotes the activation of C-H bond of methane, and increases its selective conversion, thus leading to the extraordinarily high C1 oxygenate yield of 4799 µmol gcat -1 h-1 with 97.9 % selectivity, circa 8 times higher than those modulated with AA.

Breaking Platinum Nanoparticles to Single-Atomic Pt-C4 Co-catalysts for Enhanced Solar-to-Hydrogen Conversion.

Effective transfer and utilization of the photogenerated electrons are a key factor for achieving highly efficient H2 generation by photocatalytic water splitting. Apart from the activity of the co-catalyst, the interface between the co-catalyst and semiconductor is of particular importance. Guided by DFT calculations, single-atom (SA) Pt doped carbon nitride (CN) is successfully synthesized for use as the co-catalyst to the semiconducting CuS. The catalyst system (Pt1-CN@CuS) exhibits an enhanced photocatalytic performance for water splitting with a H2 production rate of 25.4 µmol h-1 and an apparent quantum yield (AQY) of 50.3 % under the illumination of LED-530. Solar-to-hydrogen (STH) conversion efficiency is calculated to be 0.5 % under AM 1.5 illumination. This is the very first investigation of SA as the co-catalyst, which decreases the overpotential of CN during the water splitting and lowers interfacial resistance of the catalyst/co-catalyst and co-catalyst/electrolyte.

Atypical Oxygen-Bearing Copper Boosts Ethylene Selectivity toward Electrocatalytic CO2 Reduction.

Oxygen-bearing copper (OBC) has been widely studied for enabling the C-C coupling of the electrocatalytic CO2 reduction reaction (CO2RR) since this is a distinctive hallmark of strongly correlated OBC systems and may benefit many other Cu-based catalytic processes. Unresolved problems, however, include the instability of and limited knowledge regarding OBC under realistic operating conditions, raising doubts about its role in CO2RR. Here, an atypical and stable OBC catalyst with a hierarchical pore and nanograin-boundary structure was constructed and was found to exhibit efficient CO2RR for the production of ethylene with a Faradaic efficiency of 45% at a partial current density of 44.7 mA cm-2 in neutral media, and the ethylene partial current density is nearly 26 and 116 times that of oxygen-free copper (OFC) and commercial Cu foam, respectively. More importantly, the structure-activity relationship in CO2RR was explored through a comprehensive analysis of experimental data and computational techniques, thus increasing the fundamental understanding of CO2RR. A systematic characterization analysis suggests that atypical OBC (Cu4O) was formed and that it is stable even at -1.00 V [(vs the reversible hydrogen electrode (RHE)]. Density functional theory calculations show that the atypical OBC enables control over CO adsorption and dimerization, making it possible to implement a preference for the electrosynthesis of ethylene (C2) products. These results provide insight into the synthesis and structural characteristics of OBC as well as its interplay with ethylene selectivity.

In situ depth-resolved synchrotron radiation X-ray spectroscopy study of radiation-induced Au deposition.

To illustrate the process of synchrotron radiation induced reduction of tetrachloroauric solutions, a confocal synchrotron radiation X-ray spectroscopy experiments system has been introduced to monitor the depth-resolved elemental Au distribution and chemical species during the Au reduction reaction. Combining the results from confocal X-ray spectroscopy with that from X-ray contrast imaging, the mechanism of synchrotron radiation induced Au reduction, along with the process of Au deposition, were proposed. These demonstrations provide novel avenues to spatially resolved analysis of in situ solution radiolysis.

Reordering d Orbital Energies of Single-Site Catalysts for CO2 Electroreduction.

The single-site catalyst (SSC) characteristic of atomically dispersed active centers will not only maximize the catalytic activity, but also provide a promising platform for establishing the structure-activity relationship. However, arbitrary arrangements of active sites in the existed SSCs make it difficult for mechanism understanding and performance optimization. Now, a well-defined ultrathin SSC is fabricated by assembly of metal-porphyrin molecules, which enables the precise identification of the active sites for d-orbital energy engineering. The activity of as-assembled products for electrocatalytic CO2 reduction is significantly promoted via lifting up the energy level of metal d z 2 orbitals, exhibiting a remarkable Faradaic efficiency of 96 % at the overpotential of 500 mV. Furthermore, a turnover frequency of 4.21 s-1 is achieved with negligible decay over 48 h.

Unraveling the Interfacial Charge Migration Pathway at the Atomic Level in a Highly Efficient Z-Scheme Photocatalyst.

A highly efficient Z-scheme photocatalytic system constructed with 1D CdS and 2D CoS2 exhibited high photocatalytic hydrogen-evolution activity of 5.54 mmol h-1 g-1 with an apparent quantum efficiency of 10.2 % at 420 nm. More importantly, its interfacial charge migration pathway was unraveled: The electrons are efficiently transferred from CdS to CoS2 through a transition atomic layer connected by Co-S5.8 coordination, thus resulting in more photogenerated carriers participating in surface reactions. Furthermore, the charge-trapping and charge-transfer processes were investigated by transient absorption spectroscopy, which gave an estimated charge-separation yield of approximately 91.5 % and a charge-separated-state lifetime of approximately (5.2±0.5) ns in CdS/CoS2 . This study elucidates the key role of interfacial atomic layers in heterojunctions and will facilitate the development of more efficient Z-scheme photocatalytic systems.

The Flexibility of an Amorphous Cobalt Hydroxide Nanomaterial Promotes the Electrocatalysis of Oxygen Evolution Reaction.

Structural flexibility can be a desirable trait of an operating catalyst because it adapts itself to a given catalytic process for enhanced activity. Here, amorphous cobalt hydroxide nanocages are demonstrated to be a promising electrocatalyst with an overpotential of 0.28 V at 10 mA cm-2 , far outperforming the crystalline counterparts and being in the top rank of the catalysts of their kind, under the condition of electrocatalytic oxygen evolution reaction. From the direct experimental in situ and ex situ results, this enhanced activity is attributed to its high structural flexibility in terms of 1) facile and holistic transformation into catalytic active phase; 2) hosting oxygen vacancies; and 3) structure self-regulation in a real-time process. Significantly, based on plausible catalytic mechanism and computational simulation results, it is disclosed how this structural flexibility facilitates the kinetics of oxygen evolution reaction. This work deepens the understanding of the structure-activity relationship of the Co-based catalysts in electrochemical catalysis, and it inspires more applications that require flexible structures enabled by such amorphous nanomaterials.

Manganese deception on graphene and implications in catalysis.

Heteroatom-doped metal-free graphene has been widely studied as the catalyst for the oxygen reduction reaction (ORR). Depending on the preparation method and the dopants, the ORR activity varies ranging from a two-electron to a four-electron pathway. The different literature reports are difficult to correlate due to the large variances. However, due to the potential metal contamination, the origin of the ORR activity from "metal-free" graphene remains confusing and inconclusive. Here we decipher the ORR catalytic activities of diverse architectures on graphene derived from reduced graphene oxide. High angle annular dark field scanning transmission electron microscopy, X-ray absorption near edge structure, extended X-ray absorption fine structure, and trace elemental analysis methods are employed. The mechanistic origin of ORR activity is associated with the trace manganese content and reaches its highest performance at an onset potential of 0.94 V when manganese exists as a mononuclear-centered structure within defective graphene. This study exposes the deceptive role of trace metal in formerly thought to be metal-free graphene materials. It also provides insight into the design of better-performing catalyst for ORR by underscoring the coordination chemistry possible for future single-atom catalyst materials.