Identification Of Active Sites Research Articles

Targeting Glucose Metabolism in Diabetes-A Homology Modeling and Active Site Identification for Inositol Monophosphatase

Targeting Glucose Metabolism in Diabetes-A Homology Modeling and Active Site Identification for Inositol Monophosphatase

Spatially Confined Microcells: A Path toward TMD Catalyst Design.

With the ability to maximize the exposure of nearly all active sites to reactions, two-dimensional transition metal dichalcogenide (TMD) has become a fascinating new class of materials for electrocatalysis. Recently, electrochemical microcells have been developed, and their unique spatial-confined capability enables understanding of catalytic behaviors at a single material level, significantly promoting this field. This Review provides an overview of the recent progress in microcell-based TMD electrocatalyst studies. We first introduced the structural characteristics of TMD materials and discussed their site engineering strategies for electrocatalysis. Later, we comprehensively described two distinct types of microcells: the window-confined on-chip electrochemical microcell (OCEM) and the droplet-confined scanning electrochemical cell microscopy (SECCM). Their setups, working principles, and instrumentation were elucidated in detail, respectively. Furthermore, we summarized recent advances of OCEM and SECCM obtained in TMD catalysts, such as active site identification and imaging, site monitoring, modulation of charge injection and transport, and electrostatic field gating. Finally, we discussed the current challenges and provided personal perspectives on electrochemical microcell research.

Int&in: A machine learning-based web server for active split site identification in inteins.

Inteins are proteins that excise themselves out of host proteins and ligate the flanking polypeptides in an auto-catalytic process called protein splicing. In nature, inteins are either contiguous or split. In the case of split inteins, the two fragments must first form a complex for the splicing to occur. Contiguous inteins have previously been artificially split in two fragments because split inteins allow for distinct applications than contiguous ones. Even naturally split inteins have been split at unnatural split sites to obtain fragments with reduced affinity for one another, which are useful to create conditional inteins or to study protein-protein interactions. So far, split sites in inteins have been heuristically identified. We developed Int&in, a web server freely available for academic research (https://intein.biologie.uni-freiburg.de) that runs a machine learning model using logistic regression to predict active and inactive split sites in inteins with high accuracy. The model was trained on a dataset of 126 split sites generated using the gp41-1, Npu DnaE and CL inteins and validated using 97 split sites extracted from the literature. Despite the limited data size, the model, which uses various protein structural features, as well as sequence conservation information, achieves an accuracy of 0.79 and 0.78 for the training and testing sets, respectively. We envision Int&in will facilitate the engineering of novel split inteins for applications in synthetic and cell biology.

Isomerization Engineering of Oxygen-Enriched Carbon Quantum Dots for Efficient Electrochemical Hydrogen Peroxide Production.

Hydrogen peroxide (H2O2) has emerged as a kind of multi-functional green oxidants with extensive industrial utility. Oxidized carbon materials exhibit promises as electrocatalysts in the two-electron (2e-) oxygen reduction reaction (ORR) for H2O2 production. However, the precise identification and fabrication of active sites that selectively yield H2O2 present a serious challenge. Herein, a structural engineering strategy is employed to synthesize oxygen-doped carbon quantum dots (o-CQD) for the 2e- ORR. The surface electronic structure of the o-CQDs is systematically modulated by varying isomerization precursors, thereby demonstrating excellent electrocatalyst performance. Notably, o-CQD-3 emerges as the most promising candidate, showcasing a remarkable H2O2 selectivity of 96.2% (n = 2.07) at 0.68V versus RHE, coupled with a low Tafel diagram of 66.95mV dec-1. In the flow cell configuration, o-CQD-3 achieves a H2O2 productivity of 338.7mmol gcatalyst -1 h-1, maintaining consistent production stability over an impressive 120-hour duration. Utilizing in situ technology and density functional theory calculations, it is unveil that edge sites of o-CQD-3 are facilely functionalized by C-O-C groups under alkaline ORR conditions. This isomerization engineering approach advances the forefront of sustainable catalysis and provides a profound insight into the carbon-based catalyst design for environmental-friendly chemical synthesis processes.

Cu single atoms mediated multiple active site reconfiguration to trigger Dual-pathway nonradical peroxymonosulfate activation process

Developing atomically dispersed metal sites is vital to enhance the activation of peroxymonosulfate (PMS). However, for catalyst systems where single atoms and nanoclusters coexist, how to identify the independent and synergistic effects of atomic sites and investigate the possible coexistence of multiple activation mechanisms still remains a great challenge. Herein, CuSA/CoOx-CeO2 catalysts with Cu single atoms and CoOx nanoclusters were fabricated for PMS activation. The introduction of Cu single atoms led to the reconstruction and diversification of catalytic active sites of CoOx-CeO2. The synergy between CoOx nanoclusters and neighboring Cu single atoms in CuSA/CoOx-CeO2 catalyst led to the 1O2 pathway of PMS activation, while the isolated Cu atom induced the Cu(III) oxidation pathway. The introducing of adjacent Cu single atoms caused the redistribution of the site charges in CoOx nanoclusters, which enhanced the charge transfer and promoted the adsorption and activation behavior of PMS molecules. During the evolution of 1O2, the synergistic effect of Cu single atoms and CoOx nanoclusters increased the stability of the reaction intermediate state (*OO*SO3), reducing the total Gibbs free energy change (ΔG) required for 1O2 formation. Compared with the cooperative site, the isolated Cu-O4 sites exhibited stronger charge transfer capacity to PMS molecules and were more conducive to the activation of the local substrate electronic structure, facilitating the formation and stabilization of Cu(III)–OH metastable intermediates. Overall, this study demonstrated the importance about the construction of multi-site induced multipath coexisting PMS activation system and the accurate identification of active sites.

Computational Analysis and NGS for Human LDHC Complexed with NAD+ and Ethylamino Acetic Acid (Lung Cancer)

Abstract: This study presents a multidimensional exploration of the structural and functional characteristics of the human Lactate Dehydrogenase C (LDHC) complexed with NAD+ and ethylamino acetic acid (EAA), focusing on its implications in lung cancer. Leveraging data from the Protein Data Bank (PDB) and Molecular Modeling Database (MMDB), a comprehensive analysis was conducted using various computational tools and resources. Structural insights were gained through PDBsum and RasMol, elucidating molecular interactions and identifying potential drug-target sites. Sequence analysis via BLAST and Multiple Sequence Alignment provided further understanding of conserved sequences and structural motifs. Visualization and manipulation of molecular structures were facilitated by PyMOL, enabling the identification of active drug-target sites. Proteinligand docking studies using the CB-Dock2 server assessed the efficiency of LDHC complexation with NAD+. Structural validation through the SAVES server ensured the reliability of the complex structure. Additionally, biological network analysis using the STRING database revealed associations with gene ontology and structural classification of the protein, offering insights into targeted interventions in the ancestry of the protein. This comprehensive approach provides valuable insights into LDHC's role in cancer biology and offers promising avenues for therapeutic development in lung cancer.

Crystal facet engineering of K-OMS-2 for active site identification in catalytic ozone decomposition

Manganese oxide catalysts (MnOx) are expected to be utilized to catalytic ozone (O3) decomposition to curb indoor O3 pollution. However, the accumulation of oxygen-containing species (*OO) on the active site (oxygen vacancy, Ov) of MnOx limits the practical application. Herein, α-MnO2 with exposed {100} (Mn-100), {110} (Mn-110), or {310} (Mn-310) facet was synthesized, respectively. Mn-110 has preferred performance and stability, maintaining 99.9 % O3 conversion after 8 h under 35 % RH. Experimental and theoretical results indicated that the Mn-100 facet owns lower Ov content and *OO adsorption energy, exhibiting the highest specific area normalized activity. Mn-310 has a higher vacancy content and enhanced *OO adsorption energy, which resulted in a rapid accumulation of *OO species. Mn-110 has a moderate Ov content and *OO adsorption and thus exhibits optimal activity. This study hopes to point out a new optimization strategy for MnOx catalysts.

Validation of NGSand Multi-omics Approach for Active Site Identification CDK2-Associated Protein 1; Oral Cancer

Validation of NGSand Multi-omics Approach for Active Site Identification CDK2-Associated Protein 1; Oral Cancer

Structural Design of Single-Atom Catalysts for Enhancing Petrochemical Catalytic Reaction Process.

Petroleum, as the "lifeblood" of industrial development, is the important energy source and raw material. The selective transformation of petroleum into high-end chemicals is of great significance, but still exists enormous challenges. Single-atom catalysts (SACs) with 100% atom utilization and homogeneous active sites, promise a broad application in petrochemical processes. Herein, the research systematically summarizes the recent research progress of SACs in petrochemical catalytic reaction, proposes the role of structural design of SACs in enhancing catalytic performance, elucidates the catalytic reaction mechanisms of SACs in the conversion of petrochemical processes, and reveals the high activity origins of SACs at the atomic scale. Finally, the key challenges are summarized and an outlook on the design, identification of active sites, and the appropriate application of artificial intelligence technology is provided for achieving scale-up application of SACs in petrochemical process.

Structural/surface characterization of transition metal element-doped H-ZSM-5 adsorbent for CH3SH removal: identification of active adsorption sites and deactivation mechanism.

CH3SH is a potential hazard to both chemical production and human health, so controlling its emissions is an urgent priority. In this work, a series of transition metal-loaded H-ZSM-5 adsorbents (Si/Al = 25) (Cu, Fe, Co, Ni, Mn, and Zn) were synthesized through the wet impregnation method and tested for CH3SH physicochemical adsorption at 60°C. It was shown that the Cu-modified H-ZSM-5 adsorbent was much more active for CH3SH removal due to its abundant strong acid sites than other transition metal-modified H-ZSM-5 adsorbents. The detailed physicochemical properties of various modified H-ZSM-5 adsorbents were characterized by SEM, XRD, N2 physisorption, XPS, H2-TPR, and NH3-TPD. The effects of metal loading mass ratio, calcination temperature, and acid or alkali modification on the performance of the adsorbent were also investigated, and finally 20% Cu/ZSM-5 was found to have the best adsorption capacity after calcined at 350°C. Additionally, the Cu/ZSM-5 adsorbent modified by sodium bicarbonate could expose more active components, which improved the adsorbent's stability. However, the consumption and reduction of the active component Cu2+ and the accumulation of sulfate during the adsorption process are the main reasons for the deactivation of the adsorbent. In addition, the simultaneous purging of N2 + O2 can effectively restore the adsorption capacity of the deactivated adsorbent and can be used as a potential strategy to regenerate the adsorbent.

Probing Catalytic Sites and Adsorbate Spillover on Ultrathin FeO2-x Film on Ir(111) during CO Oxidation.

The spatially resolved identification of active sites on the heterogeneous catalyst surface is an essential step toward directly visualizing a catalytic reaction with atomic scale. To date, ferrous centers on platinum group metals have shown promising potential for low-temperature CO catalytic oxidation, but the temporal and spatial distribution of active sites during the reaction and how molecular-scale structures develop at the interface are not fully understood. Here, we studied the catalytic CO oxidation and the effect of co-adsorbed hydrogen on the FeO2-x/Ir(111) surface. Combining scanning tunneling microscopy (STM), isotope-labeled pulse reaction measurements, and DFT calculations, we identified both FeO2/Ir and FeO2/FeO sites as active sites with different reactivity. The trilayer O-Fe-O structure with its Moiré pattern can be fully recovered after O2 exposure, where molecular O2 dissociates at the FeO/Ir interface. Additionally, as a competitor, dissociated hydrogen migrates onto the oxide film with the formation of surface hydroxyl and water clusters down to 150 K.

Trifunctional robust electrocatalysts based on 3D Fe/N‐doped carbon nanocubes encapsulating Co4N nanoparticles for efficient battery‐powered water electrolyzers

AbstractHerein, we have designed a highly active and robust trifunctional electrocatalyst derived from Prussian blue analogs, where Co4N nanoparticles are encapsulated by Fe embedded in N‐doped carbon nanocubes to synthesize hierarchically structured Co4N@Fe/N–C for rechargeable zinc–air batteries and overall water‐splitting electrolyzers. As confirmed by theoretical and experimental results, the high intrinsic oxygen reduction reaction, oxygen evolution reaction, and hydrogen evolution reaction activities of Co4N@Fe/N–C were attributed to the formation of the heterointerface and the modulated local electronic structure. Moreover, Co4N@Fe/N–C induced improvement in these trifunctional electrocatalytic activities owing to the hierarchical hollow nanocube structure, uniform distribution of Co4N, and conductive encapsulation by Fe/N–C. Thus, the rechargeable zinc–air battery with Co4N@Fe/N–C delivers a high specific capacity of 789.9 mAh g−1 and stable voltage profiles over 500 cycles. Furthermore, the overall water electrolyzer with Co4N@Fe/N–C achieved better durability and rate performance than that with the Pt/C and IrO2 catalysts, delivering a high Faradaic efficiency of 96.4%. Along with the great potential of the integrated water electrolyzer powered by a zinc–air battery for practical applications, therefore, the mechanistic understanding and active site identification provide valuable insights into the rational design of advanced multifunctional electrocatalysts for energy storage and conversion.

Catalysis with Two-Dimensional Metal-Organic Frameworks: Synthesis, Characterization, and Modulation.

The demand for the exploration of highly active and durable electro/photocatalysts for renewable energy conversion has experienced a significant surge in recent years. Metal-organic frameworks (MOFs), by virtue of their high porosity, large surface area, and modifiable metal centers and ligands, have gained tremendous attention and demonstrated promising prospects in electro/photocatalytic energy conversion. However, the small pore sizes and limited active sites of 3D bulk MOFs hinder their wide applications. Developing 2D MOFs with tailored thickness and large aspect ratio has emerged as an effective approach to meet these challenges, offering a high density of exposed active sites, better mechanical stability, better assembly flexibility, and shorter charge and photoexcited state transfer distances compared to 3D bulk MOFs. In this review, synthesis methods for the most up-to-date 2D MOFs are first overviewed, highlighting their respective advantages and disadvantages. Subsequently, a systematic analysis is conducted on the identification and electronic structure modulation of catalytic active sites in 2D MOFs and their applications in renewable energy conversion, including electrocatalysis and photocatalysis (electro/photocatalysis). Lastly, the current challenges and future development of 2D MOFs toward highly efficient and practical electro/photocatalysis are proposed.

The discrepancy of NH3 oxidation mechanism between SAPO-34 and Cu/SAPO-34.

The difference of NH3 oxidation mechanism over SAPO-34 and Cu-SAPO-34 was studied. XRD (X-ray diffraction), SEM (scanning electron microscopy) and H2-TPR (H2-temperature programmed desorption) were conducted to estimate the Cu species distribution. The quantity of individual Cu2+ ions escalated with the elevation of silicon content in the Cu/SAPO-34 catalysts, leading to an enhancement in the activity of the NH3-SCR (ammonia-selective catalytic reduction) process. This augmentation in activity can be attributed to the increased presence of isolated Cu2+ species, which are pivotal in facilitating the catalytic reaction. In addition, the kinetic test of NH3 oxidation indicated that the CuO species were the active sites for NH3 oxidation. Specifically, the strong structural Brønsted acid sites were the NH3 oxidation active sites over the SAPO-34 support, and the NH3 reacted with the O2 on the Brønsted acid sites to produce the NO mainly. While the NH3 oxidation mechanism over Cu/SAPO-34 consisted of two steps: firstly, NH3 reacted with O2 on CuO sites or residual Brønsted acid sites to form NO as the product; subsequently, the generated NO was reduced by NH3 into N2 on isolated Cu2+ sites. Simultaneously, the isolated Cu2+ sites might demonstrate a significant function in the NH3 oxidation process to form N2. The identification of active sites and corresponding mechanism could deepen the understanding of excellent performance of NH3-SCR over the Cu/SAPO-34 catalyst at high temperature.

Local structural environment of single-atom catalysts

In this review, we discuss the catalytically active sites of single-atom catalysts regulated by modulating the metal single-atoms and coordination environment, as well as summarizing major challenges and development opportunities for the field of SACs.

Atomically precise Cu41 clusters as model catalysts: Open metal sites matter

Although the significance of open metal sites for controlling metal nanoparticle catalysis have been well-documented, the direct identification of authentic active sites remains a grand challenge. In this work, we report a new couple of “isostructural” copper nanoclusters, namely, [Cu41Cl2(2-F-C6H4S)12(CF3COO)6(PPh3)6H19]2- (1H) and [Cu41(2,5-di-Methyl-C6H3S)12(BO3)3Cl3(PPh3)6H19] (2H), from which heavy dependence of catalytic activity on coordinatively unsaturated metal sites is directly visualized. Both clusters have been characterized by various advanced techniques including high resolution mass spectroscopy (MS), ultra-violet visible spectroscopy (UV-Vis), nuclear magnetic resonance (NMR), density functional theory (DFT) calculations and X-ray single crystal diffraction. The clusters adopt a core-shell arrangement, in which the Cu29 core is grown via the face-fusion of three Cu13 units. Notably, such Cu13-based growth mode is observed for the first time for copper nanoclusters. The main difference of the two Cu41 clusters lies in the presence or absence of two additional chlorides on the surface, which in turn heavily control the exposure of metal sites. 2H with more open metal sites exhibits, as envisioned, much higher activity than 1H in catalytic hydrogenation reaction (6-fold increase in rate constant). This work thus not only represent a mode system to directly visualize the true active sites of metal nanoclusters, but also provides the atomistic evidence on highlighting the importance of exposed metal sites for controlling performance of metal nanocatalysts.

Microwave-assisted exploration of the electron configuration-dependent electrocatalytic urea oxidation activity of 2D porous NiCo2O4 spinel

Urea holds promise as an alternative water-oxidation substrate in electrolytic cells. High-valence nickel-based spinel, especially after heteroatom doping, excels in urea oxidation reactions (UOR). However, traditional spinel synthesis methods with prolonged high-temperature reactions lack kinetic precision, hindering the balance between controlled doping and highly active two-dimensional (2D) porous structures design. This significantly impedes the identification of electron configuration-dependent active sites in doped 2D nickel-based spinels. Herein, we present a microwave shock method for the preparation of 2D porous NiCo2O4 spinel. Utilizing the transient on-off property of microwave pulses for precise heteroatom doping and 2D porous structural design, non-metal doping (boron, phosphorus, and sulfur) with distinct extranuclear electron disparities serves as straightforward examples for investigation. Precise tuning of lattice parameter reveals the impact of covalent bond strength on NiCo2O4 structural stability. The introduced defect levels induce unpaired d-electrons in transition metals, enhancing the adsorption of electron-donating amino groups in urea molecules. Simultaneously, Bode plots confirm the impact mechanism of rapid electron migration caused by reduced band gaps on UOR activity. The prepared phosphorus-doped 2D porous NiCo2O4, with optimal electron configuration control, outperforms most reported spinels. This controlled modification strategy advances understanding theoretical structure-activity mechanisms of high-performance 2D spinels in UOR.

Enhancing plasma-catalytic toluene oxidation: Unraveling the role of Lewis-acid sites on δ-MnO2

The emission of volatile organic compounds (VOCs) into the air, primarily due to human activities, has caused significant environmental pollution and health concerns. In response, the development of advanced environmental catalysts is crucial, and δ-MnO2 has emerged as a promising material for efficient VOC oxidation. However, the identification of the specific active sites and the underlying oxidation mechanisms of this material remain unclear, hindering the development and optimization of high-activity catalysts. Herein, we present a strategy to remove the internal water and hydrated cations from δ-MnO2, thereby unblocking the inter-lamellar gaps and exposing the internal Lewis-acid sites, while maintaining other physical and chemical characteristics of the sample unchanged. Notably, the well-defined δ-MnO2 catalysts with more accessible interlayer Lewis-acid sites exhibited significantly enhanced catalytic activity in toluene oxidation, demonstrated in both two-stage plasma catalysis and single-stage ozonation processes. A quantitative analysis of Lewis-acid sites and initial toluene reaction rates revealed that these Lewis-acid sites serve as the active centers for toluene adsorption and activation, and the heterogeneous reaction between toluene and ozone follows the Langmuir-Hinshelwood mechanism. Moreover, in-depth analysis of byproducts showed that δ-MnO2 rich in Lewis-acid sites promoted the oxidation of intermediates, such as esters, hydrazides, and ketones, leading to a more complete toluene oxidation. This work not only fully explores the potential of δ-MnO2 as a catalyst, but also provides valuable insights into the elucidation of unknown catalytic active sites, potentially paving the way for the rational design of more efficient catalysts for VOC oxidation.

Experimental Challenges in the Electrocatalytic Benchmarking of Multicomponent Alloys

Multicomponent alloys, especially complex solid solutions (CSS), and more specifically high entropy alloys (HEA) have emerged as promising new types of electrocatalysts [1] for numerous reactions of significance for energy conversion. Their exceptional properties and the large number of degrees of freedom available for tuning their properties make CSSs promising candidates for overcoming the limitations of traditional catalysts: activity limitations imposed by the scaling, as well as stability issues.Despite the large interest they have garnered, their potential still remains to be understood and harnessed, as their electrochemical behavior still needs to be understood. Significant experimental challenges need to be addressed and widely applied standards need to be implemented in order to understand and correctly asses the electrocatalytic behavior of such catalysts. The electrochemical surface area (ECSA) determination, identification of active sites, understanding their operando behavior, effects of crystallinity [2] as well as basic experimental challenges, such as careful Ohmic drop correction, are some of the most important experimental challenges in the electrocatalytic assessment of CSSs.Here, an overview of CSS catalysts for the oxygen reduction reaction to date will be given (Figure 1A) [1]. Traditional methods used to evaluate the ECSA of well-known systems (e.g. noble metal electrodes) are discussed in relation to their use in CSS evaluation. For instance, the application of double layer charging current techniques, surface limited reactions and surface science techniques all have their advantages and drawbacks for the determination of the electrochemical surface area in terms of ease of application, size of errors introduced and reliability. Additionally, crystallinity (more generally, the effects of long- and short-range order, Figure 1B), phase separations, oxide layer growth and other caveats during electrocatalytic benchmarking of CSSs will be discussed. Figure 1

(Keynote) Competition of Oxygen and Chlorine Evolution on Oxide Surfaces – a Soft X-Ray and Dems Approach to Identification of Active Site

Anodic gas evolving reactions, e.g. oxygen evolution and chlorine evolution, are of fundamental importance both in energy storage as well as in electrolytic production of chemicals. Both reactions are of electrocatalytic nature, proceed in the same potential range and are catalyzed by the same types of electrode materials. While the oxygen evolution is thermodynamically favored the two electron chlorine evolution is kinetically preferred, namely at acid and neutral pH. This kinetic preference is industrially explored in chlor-alkali processes as well in chlorate electrolysis. The growing interest in electrolytic hydrogen production fueled by the popularity of the hydrogen as the likely replacement of fossil fuels brings up the question of the tolerance of the industrial anodes to presence of chlorides in the water intended for electrolytic hydrogen production. Such a tolerance can be best achieved by steering the selectivity of the anode between oxygen and chlorine evolution aiming eventually at the possibility of the sea water use in hydrogen producing water electrolysis. So far existing attempts at control the anode selectivity in presence of chlorides explore two principal approaches – pH control and surface engineering. While the pH related approach is rationalized by different pH sensitivity of each of the competing reaction the surface engineering related activities so far rely on trial and error approach. Qualitatively the selectivity may be controlled by either selectively promoting/suppressing each of the contributing reactions. While the literature lists attempts when the overall selectivity towards OER is apparently achieved by selective suppression of CER [1] more recent reports suggest that the actual selectivity is in fact controlled by the ability of the catalysts to support a lattice oxygen activating mechanism of the oxygen evolution process [2]. While these assignments are based on correlation of selectivity measurements with local structure and DFT modelling and a direct evidence of such a behavior is so far missing. This paper will document here the capability of the real-time and operando soft X-ray absorption spectroscopy [3] to provide this missing evidence. Anodic behavior of two type of ruthenium oxide electrodes in chloride free and chloride containing solutions will be documented by comparison of the nature and potential dependent population of the oxygen related intermediates formed at anode surface in the potential range of oxygen and chlorine evolution in acid media (pH=1) and combined with DEMS data to identify the active sites for each contributing electrode reaction.