Engineering of the Lrp/AsnC-type transcriptional regulator DecR as a genetically encoded biosensor for multilevel optimization of L-cysteine biosynthesis pathway in Escherichia coli.

L-cysteine is an important sulfur-containing amino acid being difficult to produce by microbial fermentation. Due to the lack of high-throughput screening methods, existing genetically engineered bacteria have been developed by simply optimizing the expression of L-cysteine-related genes one by one. To overcome this limitation, in this study, a biosensor-based approach for multilevel biosynthetic pathway optimization of L-cysteine from the DecR regulator variant of Escherichia coli was applied. Through protein engineering, we obtained the DecRN29Y/C81E/M90Q/M99E variant-based biosensor with improved specificity and an 8.71-fold increase in dynamic range. Using the developed biosensor, we performed high-throughput screening of the constructed promoter and RBS combination library, and successfully obtained the optimized strain, which resulted in a 6.29-fold increase in L-cysteine production. Molecular dynamics (MD) simulations and electrophoretic mobility shift analysis (EMSA) showed that the N29Y/C81E/M90Q/M99E variant had enhanced induction activity. This enhancement may be due to the increased binding of the variant to DNA in the presence of L-cysteine, which enhances transcriptional activation. Overall, our biosensor-based strategy provides a promising approach for optimizing biosynthetic pathways at multiple levels. The successful implementation of this strategy demonstrates its potential for screening improved recombinant strains.

Mechanism of Particle-Mediated Inhibition of Demetalation for Single-Atom Catalytic Sites in Acidic Electrochemical Environments.

Demetalation, caused by the electrochemical dissolution of metal atoms, poses a significant challenge to the practical application of single-atom catalytic sites (SACSs) in proton exchange membrane-based energy technologies. One promising approach to inhibit SACS demetalation is the use of metallic particles to interact with SACSs. However, the mechanism underlying this stabilization remains unclear. In this study, we propose and validate a unified mechanism by which metal particles can inhibit the demetalation of Fe SACSs. Metal particles act as electron donors, decreasing the Fe oxidation state by increasing the electron density at the FeN4 position, thereby strengthening the Fe-N bond, and inhibiting electrochemical Fe dissolution. Different types, forms, and contents of metal particles increase the Fe-N bond strength to varying extents. A linear correlation between the Fe oxidation state, Fe-N bond strength, and electrochemical Fe dissolution amount supports this mechanism. Our screening of a particle-assisted Fe SACS led to a 78% reduction in Fe dissolution, enabling continuous operation for up to 430 h in a fuel cell. These findings contribute to the development of stable SACSs for energy applications.

Mechanism of Cations Suppressing Proton Diffusion Kinetics for Electrocatalysis.

Proton transfer is crucial for electrocatalysis. Accumulating cations at electrochemical interfaces can alter the proton transfer rate and then tune electrocatalytic performance. However, the mechanism for regulating proton transfer remains ambiguous. Here, we quantify the cation effect on proton diffusion in solution by hydrogen evolution on microelectrodes, revealing the rate can be suppressed by more than 10 times. Different from the prevalent opinions that proton transport is slowed down by modified electric field, we found water structure imposes a more evident effect on kinetics. FTIR test and path integral molecular dynamics simulation indicate that proton prefers to wander within the hydration shell of cations rather than to hop rapidly along water wires. Low connectivity of water networks disrupted by cations corrupts the fast-moving path in bulk water. This study highlights the promising way for regulating proton kinetics via a modified water structure.

Reaction Mechanism and Selectivity Tuning of Propene Oxidation at the Electrochemical Interface.

Electrochemical conversion of propene is a promising technique for manufacturing commodity chemicals by using renewable electricity. To achieve this goal, we still need to develop high-performance electrocatalysts for propene electrooxidation, which highly relies on understanding the reaction mechanism at the molecular level. Although the propene oxidation mechanism has been well investigated at the solid/gas interface under thermocatalytic conditions, it still remains elusive at the solid/liquid interface under an electrochemical environment. Here, we report the mechanistic studies of propene electrooxidation on PdO/C and Pd/C catalysts, considering that the Pd-based catalyst is one of the most promising electrocatalytic systems. By electrochemical in situ attenuated total reflection Fourier transform infrared spectroscopy, a distinct reaction pathway was observed compared with conventional thermocatalysis, emphasizing that propene can be dehydrogenated at a potential higher than 0.80 V, and strongly adsorb via µ-C═CHCH3 and µ3-η2-C═CHCH3 configuration on PdO and Pd, respectively. The µ-C═CHCH3 is via bridge bonds on adjacent Pd and O atoms on PdO, and it can be further oxidized by directly taking surface oxygen from PdO, verified by the H218O isotope-edited experiment. A high surface oxygen content on PdO/C results in a 3 times higher turnover frequency than that on Pd/C for converting propene into propene glycol. This finding highlights the different reaction pathways under an electrochemical environment, which sheds light on designing next-generation electrocatalysts for propene electrooxidation.

High CO-Tolerant Ru-Based Catalysts by Constructing an Oxide Blocking Layer.

CO poisoning of Pt-group metal catalysts is a long-standing problem, particularly for hydrogen oxidation reaction in proton exchange membrane fuel cells. Here, we report a catalyst of Ru oxide-coated Ru supported on TiO2 (Ru@RuO2/TiO2), which can tolerate 1-3% CO, enhanced by about 2 orders of magnitude over the classic PtRu/C catalyst, for hydrogen electrooxidation in a rotating disk electrode test. This catalyst can work stably in 1% CO/H2 for 50 h. About 20% of active sites can survive even in a pure CO environment. The high CO tolerance is not via a traditional bifunctional mechanism, i.e., oxide promoting CO oxidation, but rather via hydrous metal oxide shell blocking CO adsorption. An ab initio molecular dynamics (AIMD) simulation indicates that water confined in grain boundaries of the Ru oxide layer and Ru surface can suppress the diffusion and adsorption of CO. This oxide blocking layer approach opens a promising avenue for the design of high CO-tolerant electrocatalysts for fuel cells.

p-d Orbital Hybridization Induced by a Monodispersed Ga Site on a Pt3 Mn Nanocatalyst Boosts Ethanol Electrooxidation.

Constructing monodispersed metal sites in heterocatalysis is an efficient strategy to boost their catalytic performance. Herein, a new strategy using monodispersed metal sites to tailor Pt-based nanocatalysts is addressed by engineering unconventional p-d orbital hybridization. Thus, monodispersed Ga on Pt3 Mn nanocrystals (Ga-O-Pt3 Mn) with high-indexed facets was constructed for the first time to drive ethanol electrooxidation reaction (EOR). Strikingly, the Ga-O-Pt3 Mn nanocatalyst shows an enhanced EOR performance with achieving 8.41 times of specific activity than that of Pt/C. The electrochemical in situ Fourier transform infrared spectroscopy results and theoretical calculations disclose that the Ga-O-Pt3 Mn nanocatalyst featuring an unconventional p-d orbital hybridization not only promote the C-C bond-breaking and rapid oxidation of -OH of ethanol, but also inhibit the generation of poisonous CO intermediate species. This work discloses a promising strategy to construct a novel nanocatalysts tailored by monodispersed metal site as efficient fuel cell catalysts.

Porous Carbon Membrane-Supported Atomically Dispersed Pyrrole-Type FeN4 as Active Sites for Electrochemical Hydrazine Oxidation Reaction.

The rational design of catalytically active sites in porous materials is essential in electrocatalysis. Herein, atomically dispersed Fe-Nx sites supported by hierarchically porous carbon membranes are designed to electrocatalyze the hydrazine oxidation reaction (HzOR), one of the key techniques in electrochemical nitrogen transformation. The high intrinsic catalytic activity of the Fe-Nx single-atom catalyst together with the uniquely mixed micro-/macroporous membrane support positions such an electrode among the best-known heteroatom-based carbon anodes for hydrazine fuel cells. Combined with advanced characterization techniques, electrochemical probe experiments, and density functional theory calculation, the pyrrole-type FeN4 structure is identified as the real catalytic site in HzOR.

Accurate prediction of species-specific 2-hydroxyisobutyrylation sites based on machine learning frameworks.

Lysine 2-hydroxyisobutyrylation (Khib) is a newly discovered post-translational modification (PTM) across eukaryotes and prokaryotes in recent years, which plays a significant role in diverse cellular functions. Accurate prediction of Khib sites is a first-crucial step to decipher its molecular mechanism and urgently needed. In this work, based on a large benchmark datasets in multi-species, a novel online species-specific prediction tool, namely KhibPred, was developed to identify Khib sites. Four types of feature strategies, including sequence-based information, physicochemical properties and evolutionary-derived information, were applied to represent a wide range of protein sequences, and the random forest was used to build the optimal feature datasets. Moreover, six representative machine learning (ML) methods were trained and comprehensively discussed and compared for each organism. Data analyses suggested that the unique protein sequence preferences were discovered for each species. When evaluated on independent test datasets, the area under the receiver operating characteristic curves (AUCs) achieved 0.807, 0.781, 0.825 and 0.831 for Saccharomyces cerevisiaes, Physcomitrella patens, Rice Seeds and HeLa cells, respectively. The satisfactory results imply that KhibPred is a promising computational tool. The online predictor can be freely available at: http://bioinfo.ncu.edu.cn/KhibPred.aspx.

Versatile, Robust, and Facile Approach for in Situ Monitoring Electrocatalytic Processes through Liquid Electrochemical NMR Spectroscopy.

With the strength of liquid nuclear magnetic resonance (NMR) to noninvasively and specifically realize the structural elucidation and quantitative analysis of small organic molecules, in principle, liquid in situ electrochemical-NMR (EC-NMR) possesses great advantages for detecting dissolved species during the electrochemical process. However, the intrinsic incompatibilities between the coupling techniques as well as the sophisticated setups modification still limit the applications toward a wide range. To overcome these bottlenecks, herein we propose an easy-to-construct design with good compatibility and presenting improved electrochemical and NMR performances. As proof of concept, model experiments of alcohol electrooxidation were performed to confirm the capacity of this device for liquid in situ EC-NMR study. The temporal evolution of both the product and the current distributions can be reliably recorded to aid mechanistic and kinetic understanding of electrocatalysis. The depiction of the selective electrooxidation reveals the surface structure-catalytic functionality. This work demonstrates the universality and effectivity of the proposed platform to develop the liquid in situ EC-NMR technique as a useful tool for the dynamic analysis of electrochemical processes at a molecular level.

Electrochemical CO2 reduction on Cu and Au electrodes studied using in situ sum frequency generation spectroscopy.

As an important pathway for energy storage and a key reaction in the carbon cycle, the CO2 electrochemical reduction reaction has recently gained significant interest. A variety of catalysts have been used to approach this topic experimentally and theoretically; however, the molecular level insight into the reaction mechanism is lacking due to the complexity of the surface processes and the challenges in probing the intermediate species. In this study, CO2 reduction reactions on polycrystalline Cu and Au electrodes were investigated in 0.1 M CO2-saturated NaHCO3 solution. In situ sum frequency generation (SFG) spectroscopy has been adopted to access the intermediates and products on the metal electrodes. On the Au electrode, only linearly adsorbed CO could be detected, and the reduction produced no hydrocarbon species. On the Cu electrode, C-H stretching vibrations corresponding to surface-adsorbed ethoxy species were observed, but no CO vibrations can be detected with SFG. The results revealed that the CO randomly adsorbed on the Cu surface, and the multiple orientations of the adsorbed species may be the reason for the formation of C-C bonding. These results demonstrate direct molecular level evidence for different reaction pathways on the Cu and Au electrodes.

Synergy between Plasmonic and Electrocatalytic Activation of Methanol Oxidation on Palladium-Silver Alloy Nanotubes.

Localized surface plasmon resonance (LSPR) excitation of noble metal nanoparticles has been shown to accelerate and drive photochemical reactions. Here, LSPR excitation is shown to enhance the electrocatalysis of a fuel-cell-relevant reaction. The electrocatalyst consists of Pdx Ag alloy nanotubes (NTs), which combine the catalytic activity of Pd toward the methanol oxidation reaction (MOR) and the visible-light plasmonic response of Ag. The alloy electrocatalyst exhibits enhanced MOR activity under LSPR excitation with significantly higher current densities and a shift to more positive potentials. The modulation of MOR activity is ascribed primarily to hot holes generated by LSPR excitation of the Pdx Ag NTs.

A Lattice-Oxygen-Involved Reaction Pathway to Boost Urea Oxidation.

The electrocatalytic urea oxidation reaction (UOR) provides more economic electrons than water oxidation for various renewable energy-related systems owing to its lower thermodynamic barriers. However, it is limited by sluggish reaction kinetics, especially by CO2 desorption steps, masking its energetic advantage compared with water oxidation. Now, a lattice-oxygen-involved UOR mechanism on Ni4+ active sites is reported that has significantly faster reaction kinetics than the conventional UOR mechanisms. Combined DFT, 18 O isotope-labeling mass spectrometry, and in situ IR spectroscopy show that lattice oxygen is directly involved in transforming *CO to CO2 and accelerating the UOR rate. The resultant Ni4+ catalyst on a glassy carbon electrode exhibits a high current density (264 mA cm-2 at 1.6 V versus RHE), outperforming the state-of-the-art catalysts, and the turnover frequency of Ni4+ active sites towards UOR is 5 times higher than that of Ni3+ active sites.

In Situ Monitoring Potential-Dependent Electrochemical Process by Liquid NMR Spectroelectrochemical Determination: A Proof-of-Concept Study.

We report the design and the performance of a two-chamber thin-layer electrochemical device for in situ potential-dependent liquid NMR measurement. Liquid NMR spectra, simultaneously recorded with cyclic voltammetry (CV), have been obtained to reveal molecular changes with potentials scanning. As a proof of concept, redox properties of 1,4-benzoquinone based systems have been investigated, and a π dimerization has been identified by combining both in situ and ex situ NMR analyses. This work provides a new approach for spectroelectrochemistry, which will contribute to developing electrochemical NMR (EC-NMR) as an important tool for the analysis of electrochemical process at a molecular level.

Interfacial electronic effects control the reaction selectivity of platinum catalysts.

Tuning the electronic structure of heterogeneous metal catalysts has emerged as an effective strategy to optimize their catalytic activities. By preparing ethylenediamine-coated ultrathin platinum nanowires as a model catalyst, here we demonstrate an interfacial electronic effect induced by simple organic modifications to control the selectivity of metal nanocatalysts during catalytic hydrogenation. This we apply to produce thermodynamically unfavourable but industrially important compounds, with ultrathin platinum nanowires exhibiting an unexpectedly high selectivity for the production of N-hydroxylanilines, through the partial hydrogenation of nitroaromatics. Mechanistic studies reveal that the electron donation from ethylenediamine makes the surface of platinum nanowires highly electron rich. During catalysis, such an interfacial electronic effect makes the catalytic surface favour the adsorption of electron-deficient reactants over electron-rich substrates (that is, N-hydroxylanilines), thus preventing full hydrogenation. More importantly, this interfacial electronic effect, achieved through simple organic modifications, may now be used for the optimization of commercial platinum catalysts.

Structure Design and Performance Tuning of Nanomaterials for Electrochemical Energy Conversion and Storage.

The performance of nanomaterials in electrochemical energy conversion (fuel cells) and storage (secondary batteries) strongly depends on the nature of their surfaces. Designing the structure of electrode materials is the key approach to achieving better performance. Metal or metal oxide nanocrystals (NCs) with high-energy surfaces and open surface structures have attained significant attention in the past decade since such features possess intrinsically exceptional properties. However, they are thermodynamically metastable, resulting in a huge challenge in their shape-controlled synthesis. The tuning of material structure, design, and performance on the nanoscale for electrochemical energy conversion and storage has attracted extended attention over the past few years. In this Account, recent progress made in shape-controlled synthesis of nanomaterials with high-energy surfaces and open surface structures using both electrochemical methods and surfactant-based wet chemical route are reviewed. In fuel cells, the most important catalytic materials are Pt and Pd and their NCs with high-energy surfaces of convex or concave morphology. These exhibit remarkable activity toward electrooxidation of small organic molecules, such as formic acid, methanol, and ethanol and so on. In practical applications, the successful synthesis of Pt NCs with high-energy surfaces of small sizes (sub-10 nm) realized a superior high mass activity. The electrocatalytic performances have been further boosted by synergetic effects in bimetallic systems, either through surface decoration using foreign metal atoms or by alloying in which the high-index facet structure is preserved and the electronic structure of the NCs is altered. The intrinsic relationship of high electrocatalytic performance dependent on open structure and high-energy surface is also valid for (metal) oxide nanomaterials used in Li ion batteries (LIB). It is essential for the anode nanomaterials to have optimized structures to keep them more stable during the charge/discharge processes for reducing damaging volume expansion via intercalation and subsequent reduced battery lifetime. In the case of cathodes, tuning the surface structure of nanomaterials should be one of the most beneficial strategies to enhance the capacity and rate performance. In addition, metal oxides with unique defective structure of high catalytic activity and carbon materials of porous structure for facilitating fast Li+ diffusion paths and efficiently trapping polysulfide are most important approached and employed in Li-O2 battery and Li-S battery, respectively. In summary, significant progress has already been made in the electrocatalytic field, and likely emerging techniques based on NCs enclosed with high-energy surfaces and high-index facets could provide a promising platform to investigate the surface structure-catalytic functionality at nanoscale, thus shedding light on the rational design of practical catalysts with high activity, selectivity, and durability for energy conversion and storage.

Seeds and Potentials Mediated Synthesis of High-Index Faceted Gold Nanocrystals with Enhanced Electrocatalytic Activities.

Because high-index facets (HIFs) possess high surface energy, the metal nanoparticles enclosed with HIFs are eliminated during their growth in a conventional shape-controlled synthesis due to the thermodynamics that drives the particles minimizing their total surface energy. This study develops a double-step potential method to prepare an unprecedentedly stellated Au nanocrystals (NCs) bounded by high-index {711} and {331} facets in deep eutectic solvent (DES) medium. The formation of Au NCs bounded by HIFs was systematically studied. It has demonstrated that the shapes of Au NCs are strongly dependent on the size of seeds and the growth potentials as well as the urea adsorbates in the DES. By adjusting the size of seeds and the growth potentials, the stellated Au NCs can be transformed into concave hexoctahedra (HOH) with high-index {421} facets and concave trisoctahedra (TOH) with high-index {991} facets. The electrocatalytic activities of the as-prepared Au NCs are evaluated by glucose oxidation. Thanks to HIFs having high density of atomic steps and kinks, the stellated, TOH, and HOH Au NCs exhibit higher electrocatalytic activity than that of the polycrystalline Au electrode, demonstrating that the steps and kinks serve as the active sites and play an important role in glucose electro-oxidation.

Computing Prediction and Functional Analysis of Prokaryotic Propionylation.

Identification and systematic analysis of candidates for protein propionylation are crucial steps for understanding its molecular mechanisms and biological functions. Although several proteome-scale methods have been performed to delineate potential propionylated proteins, the majority of lysine-propionylated substrates and their role in pathological physiology still remain largely unknown. By gathering various databases and literatures, experimental prokaryotic propionylation data were collated to be trained in a support vector machine with various features via a three-step feature selection method. A novel online tool for seeking potential lysine-propionylated sites (PropSeek) ( http://bioinfo.ncu.edu.cn/PropSeek.aspx ) was built. Independent test results of leave-one-out and n-fold cross-validation were similar to each other, showing that PropSeek is a stable and robust predictor with satisfying performance. Meanwhile, analyses of Gene Ontology, Kyoto Encyclopedia of Genes and Genomes pathways, and protein-protein interactions implied a potential role of prokaryotic propionylation in protein synthesis and metabolism.

Electrochemically Seed-Mediated Synthesis of Sub-10 nm Tetrahexahedral Pt Nanocrystals Supported on Graphene with Improved Catalytic Performance.

Controlling the surface structure of Pt nanocrystals (NCs), especially creating high-index facets with abundant active step sites, is an effective approach to enhance catalytic performances. However, the available high-index faceted Pt NCs have large particle sizes, which severely impedes their practical applications. In this study, we reported a new electrochemically seed-mediated method, by which sub-10 nm tetrahexahedral Pt NCs (THH Pt NCs) enclosed with {210} high-index facets supported on graphene were synthesized. Pt nanoparticles of ∼3 nm in size as high-density crystal seeds play a key role in the small-sized control. The obtained THH Pt NCs exhibited a higher mass activity than commercial Pt/C catalyst for ethanol electrooxidation. We further demonstrated that this method is also valid for reshaping commercial Pt/C, to create high-index facets on surfaces and thus to improve both mass activity and stability.

S-Doping of an Fe/N/C ORR Catalyst for Polymer Electrolyte Membrane Fuel Cells with High Power Density.

Fe/N/C is a promising non-Pt electrocatalyst for the oxygen reduction reaction (ORR), but its catalytic activity is considerably inferior to that of Pt in acidic medium, the environment of polymer electrolyte membrane fuel cells (PEMFCs). An improved Fe/N/C catalyst (denoted as Fe/N/C-SCN) derived from Fe(SCN)3, poly-m-phenylenediamine, and carbon black is presented. The advantage of using Fe(SCN)3 as iron source is that the obtained catalyst has a high level of S doping and high surface area, and thus exhibits excellent ORR activity (23 A g(-1) at 0.80 V) in 0.1 M H2SO4 solution. When the Fe/N/C-SCN was applied in a PEMFC as cathode catalyst, the maximal power density could exceed 1 W cm(-2).

Phenylenediamine-based FeN(x)/C catalyst with high activity for oxygen reduction in acid medium and its active-site probing.

High-temperature pyrolyzed FeN(x)/C catalyst is one of the most promising nonprecious metal electrocatalysts for oxygen reduction reaction (ORR). However, it suffers from two challenging problems: insufficient ORR activity and unclear active site structure. Herein, we report a FeN(x)/C catalyst derived from poly-m-phenylenediamine (PmPDA-FeN(x)/C) that possesses high ORR activity (11.5 A g(-1) at 0.80 V vs RHE) and low H2O2 yield (<1%) in acid medium. The PmPDA-FeN(x)/C also exhibits high catalytic activity for both reduction and oxidation of H2O2. We further find that the ORR activity of PmPDA-FeN(x)/C is not sensitive to CO and NO(x) but can be suppressed significantly by halide ions (e.g., Cl(-), F(-), and Br(-)) and low valence state sulfur-containing species (e.g., SCN(-), SO2, and H2S). This result reveals that the active sites of the FeN(x)/C catalyst contains Fe element (mainly as Fe(III) at high potentials) in acid medium.