Active Site Microenvironment Research Articles

Decrypting the Influence of Axial Coordination on the Electronic Microenvironment of Co-N 5 Site for Enhanced Electrocatalytic Reaction

Decrypting the Influence of Axial Coordination on the Electronic Microenvironment of Co-N ₅ Site for Enhanced Electrocatalytic Reaction

Environment Molecules Boost the Chemoselective Hydrogenation of Nitroarenes on Cobalt Single-Atom Catalysts

Single-atom catalysts (SACs) have received intensive interest due to the utmost atom utilization and unique catalytic behaviors. However, the catalytic mechanism of SACs is still unclear, especially in the reactions involving multiple substrates. Here, we report that the environment moieties, protic solvents, and external bases can boost the cobalt SAC-catalyzed chemoselective hydrogenation of nitroarenes. Systematical studies clearly reveal that the heterolysis of H2 between the metal center and the neighboring coordination sphere is significantly facilitated via the H-shuttling or deprotonation route with the participation of protic solvents or bases. Besides, the derived single-atom cobalt hydride species are confirmed to be specifically reactive for the reduction of the nitro group, affording a superior activity and general chemoselectivity in the hydrogenation of various nitroarenes. Finally, a catalytic cycle is proposed to elucidate the activity origin of SACs, which sheds light on the rational design of SACs by engineering the microenvironment of active sites.

Engineering d-band center of iron single atom site through boron incorporation to trigger the efficient bifunctional oxygen electrocatalysis

Modulating the microenvironment of single-metal active sites holds excellent promises for developing highly efficiently oxygen electrocatalysts. Herein, by combining theoretical predictions and experiments, we reported a general strategy to engineer the electronic properties of iron-nitrogen-carbon (FeN4/C) catalysts via the incorporation of the boron (B) atom for achieving improved catalytic activity in oxygen electrocatalysis. Our theoretical results revealed that B modulation effectively tunes the d-band center of the iron (Fe) active site to optimize its adsorption strength with oxygenated species, greatly enhancing oxygen reduction reaction (ORR) and oxygen evolution reactions (OER) activity. Our experimental measurements then confirmed the above theoretical predictions: the as-synthesized B-doped FeN4/C (Fe-N4-B) material can perform as an eligible bifunctional catalyst for ORR and OER in alkaline media, and its catalytic activity even outperforms the commercial noble metal benchmarks. The present findings provide a promising strategy to further design the advanced catalysts for a wide range of electrochemical applications.

(Keynote, Digital Presentation) Environmental Remediation and Conversion of Pollutants to High-Value Chemicals by Integrated Adsorption-Separation-Electrocatalysis Processes

With rapidly growing industrial and economic activities, low-level pollutants, such as nitrate, urea, etc. in air, surface and ground water, have been increasing due to release of fertilizers and pesticides from industry, agriculture, and domestic sewage. It is promising to remove these pollutants and subsequently produce high-value chemicals by electrocatalysis but suffers from low efficiency. Recently, we have exploited several strategies, such as the built-in-electric field, local coordination symmetry, enhanced adsorption-separation interface and substrate geometry, to modulate the microenvironment of active sites on electrocatalysts, facilitating interfacial accumulation of the low-concentration pollutants. These have resulted in remarkable enhancement of the pollutant removal efficiency as well as improvement of yield of high-value products. In this talk, we will report our progress in separation and electrocatalytic removal of low-concentration pollutants and conversion of pollutant to high-value products.

Tailoring Coordination Microenvironment of Cu(I) in Metal–Organic Frameworks for Enhancing Electroreduction of CO2to CH4

AbstractThe coordination microenvironment of metal active sites in metal–organic frameworks (MOFs) plays a crucial role in its performance for electrochemical CO2reduction reaction (CO2RR). However, it remains a challenge to clarify the structure–performance relationship for CO2RR catalyzed by MOFs. Herein, a series of MOFs with different coordination microenvironments of Cu(I) sites (CuCl, CuBr, and CuI) to evaluate their performances for CO2RR is synthesized. With the increasing radius of halogen atom, the CO2adsorption capacity increases and d‐band center of Cu positively shifts to the Fermi level, leading to enhance the selectivity of CO2to CH4conversion. CuI gives the highest total Faradaic efficiency (FE) of 83.2%, with a FE of CH4up to 57.2% and CH4partial current density of 60.7 mA cm−2at −1.08 V versus reversible hydrogen electrode. Theoretical calculations reveal that the shifted d‐band center of Cu site contributes to reduced formation energies of *CH2O and *CH3O intermediates, which is the potential‐determining step of CO2RR and thus facilitates the electrocatalytic CO2reduction to CH4. This study opens a new avenue for studying the relationship between the coordination microenvironment of active site and electroreduction reaction performance of MOFs.

Highly stable and tunable peptoid/hemin enzymatic mimetics with natural peroxidase-like activities

Developing tunable and stable peroxidase mimetics with high catalytic efficiency provides a promising opportunity to improve and expand enzymatic catalysis in lignin depolymerization. A class of peptoid-based peroxidase mimetics with tunable catalytic activity and high stability is developed by constructing peptoids and hemins into self-assembled crystalline nanomaterials. By varying peptoid side chain chemistry to tailor the microenvironment of active sites, these self-assembled peptoid/hemin nanomaterials (Pep/hemin) exhibit highly modulable catalytic activities toward two lignin model substrates 2,2-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) and 3,3’,5,5’-tetramethylbenzidine. Among them, a Pep/hemin complex containing the pyridyl side chain showed the best catalytic efficiency (Vmax/Km = 5.81 × 10−3 s−1). These Pep/hemin catalysts are highly stable; kinetics studies suggest that they follow a peroxidase-like mechanism. Moreover, they exhibit a high efficacy on depolymerization of a biorefinery lignin. Because Pep/hemin catalysts are highly robust and tunable, we expect that they offer tremendous opportunities for lignin valorization to high value products.

Microenvironment engineering of supported metal nanoparticles for chemoselective hydrogenation.

Selective hydrogenation with supported metal catalysts widely used in the production of fine chemicals and pharmaceuticals often faces a trade-off between activity and selectivity, mainly due to the inability to adjust one factor of the active sites without affecting other factors. In order to solve this bottleneck problem, the modulation of the microenvironment of active sites has attracted more and more attention, inspired by the collaborative catalytic mode of enzymes. In this perspective, we aim to summarize recent advances in the regulation of the microenvironment surrounding supported metal nanoparticles (NPs) using porous materials enriched with organic functional groups. Insights on how the microenvironment induces the enrichment, oriented adsorption and activation of substrates through non-covalent interaction and thus determines the hydrogenation activity and selectivity will be particularly discussed. Finally, a brief summary will be provided, and challenges together with a perspective in microenvironment engineering will be proposed.

Surface microenvironment optimization‐ induced robust oxygen reduction for neutral zinc‐air batteries

AbstractNeutral zinc‐air batteries (ZABs) are promising candidates for the next‐generation power devices with considerably elongated lifetime comparing to conventional alkaline ZABs. However, neutral cathodic oxygen reduction reaction (ORR) is seriously limited by the mass transfer efficiency of hydroxyl due to insufficient interfacial chemical potential‐gradient between catalytic layer and electrolyte. Herein, we highlight that electrochemical oxidation‐induced surface microenvironment optimization could realize optimal chemical potential‐gradient around catalytic sites and bring outstanding neutral ORR activity. The electrodeposited sub‐nano Pt decorated surface‐microenvironment‐optimized Co2N samples (denoted as Pt‐SMO‐Co2N NWs) possessed 92 and 338 mV higher half‐wave potential than commercial Pt/C and pristine Co2N in 0.2 M PBS. As for neutral ZABs, Pt‐SMO‐Co2N NWs cathode delivers a power density of 67.9 mW*cm−2 and displays negligible decay after nearly 80 h stability test at 20 mA*cm−2. In‐depth characterization proposes that remarkable performance improvement originates from optimized microenvironment, which increases the surface chemical potential gradient and facilitates proton coupled electron transfer during ORR. We anticipated that such synergetic optimization of microenvironment and intrinsic activity of active sites is an effective strategy which may be extended to the catalytic reactions beyond ORR.Key points We demonstrated surface microenvironment optimization via in‐situ electrochemical oxidation as an effective way to design highly active ORR catalysts. Surface microenvironment optimization realized significantly enhanced ORR and Zn‐air battery performance in neutral media. Based on ideal material platform, the key role of activating H2O and facilitating proton transfer process in ORR catalysis was revealed.

Constitutional Dynamic Inhibition/Activation of Carbonic Anhydrases.

In this review we consider one important member of the metalloenzymes family, the carbonic anhydrase (CA), involved in the treatment of several common diseases. Different approaches have emerged to regulate the activity of CA, mostly acting on the inner catalytic active site or outer microenvironment of the enzyme, leading to inhibition or activation of CA. In recent years, gradually increased attention has focused on the adoption of constitutional dynamic chemistry (CDC) strategies for the screening and discovery of potent inhibitors or activators. The participation of reversible covalent bonds enabled the enzyme itself to select the optimal ligands obtained from diverse building blocks with comparatively higher degree of variety, resulting in the fittest recognition of enzyme ligands from complex dynamic systems. With the increasing implementation of CDC for enzyme targets, it shows great potential for drug discovery or CO2 capture applications.

Structural Basis for the Diminished Ligand Binding and Catalytic Ability of Human Fetal-Specific CYP3A7.

Cytochrome P450 3A7 (CYP3A7) is a fetal/neonatal liver enzyme that participates in estriol synthesis, clearance of all-trans retinoic acid, and xenobiotic metabolism. Compared to the closely related major drug-metabolizing enzyme in adult liver, CYP3A4, the ligand binding and catalytic capacity of CYP3A7 are substantially reduced. To better understand the structural basis for these functional differences, the 2.15 Å crystal structure of CYP3A7 has been solved. Comparative analysis of CYP3A enzymes shows that decreased structural plasticity rather than the active site microenvironment defines the ligand binding ability of CYP3A7. In particular, a rotameric switch in the gatekeeping amino acid F304 triggers local and long-range rearrangements that transmit to the F-G fragment and alter its interactions with the I-E-D-helical core, resulting in a more rigid structure. Elongation of the β3-β4 strands, H-bond linkage in the substrate channel, and steric constraints in the C-terminal loop further increase the active site rigidity and limit conformational ensemble. Collectively, these structural distinctions lower protein plasticity and change the heme environment, which, in turn, could impede the spin-state transition essential for optimal reactivity and oxidation of substrates.

Effectively Regulating the Microenvironment of Atomically Dispersed Rh through Co and Pi to Promote the Selectivity in Olefin Hydroformylation.

In the study of heterogeneity of homogeneous processes, effective control of the microenvironment of active sites is a reliable means to improve the selectivity of products. Here, we develop a high-performance Rh-based atomically dispersed catalyst for olefin hydroformylation by controlling the electronic environment and spatial distribution of active metals on the supports, which is achieved through wet impregnation of Rh on ZnO modified with Pi and Co. Various characterizations demonstrate that Co weakens Rh-CO interactions and Pi promotes the formation of atomically dispersed Rh, which thereby improves the selectivity of linear aldehydes in hydroformylation. This strategy of rationally designing the local microenvironment of active metals is important to optimize the catalytic performance.

Control of Ti active-site microenvironment in titanosilicate catalysts and its effect on oxidation pathways

The titanium (Ti) active-site microenvironment in titanosilicates is critical for oxidation performance, since it could influence oxidation pathways of the activation of H2O2, the stability of Ti−OOH species and the transfer ability of active “O” to reactant. Here, four kinds of Ti active sites in MWW-type titanosilicates were designed controllably by acid or alkali treatments, and their influences on oxidation pathways were explored. Through a series of characterizations, these microenvironments were identified, and they present different oxidation activities in this order: Ti(OSi)4(OTiO5)2 << Ti(OSi)4 < Ti(OSi)3OH < Ti(OSi)3OH(HO−Si)n. Ti(OSi)4(OTiO5)2 species cannot activate H2O2 because the framework tetrahedral Ti species in titanosilicates are shielded by extra-framework “OTiO5” (TiO6) species, leading to its inactivation in oxidation reactions. As the acid-treatment process washes off extra-framework TiO6 species, the obtained Ti(OSi)4 species are able to activate H2O2 and present an improved catalytic activity. With prolonging the acid treatment time, the Ti(OSi)3OH species is formed, and its stronger Lewis acidity contributes to the activation of H2O2 for Ti−OOH species formation. Further, upon treatment of Ti-MWW with alkali, the density of Si−OH groups near Ti active sites increases, which promotes the activation of H2O2 and stability of Ti−OOH species, simultaneously. These observations provide new ideas for designing Ti active-site microenvironment, which are expected to contribute significantly to the control of oxidation pathways.

Designing the Secondary Coordination Sphere in Small-Molecule Catalysis

AbstractThe application of secondary-sphere interactions in catalysis was inspired by the hierarchical arrangement of the microenvironment of metalloprotein active sites and has been adopted mainly in organometallic catalysis. The study of such interactions has enabled the deliberate orientation of reaction components, leading to control over reactivity and selectivity by design. Although not as common, such interaction can play a decisive role in organocatalysis. Herein, we present several examples of small-molecule organometallic- and organocatalysis, highlighting the advantages offered by carefully designing the secondary sphere.1 Introduction2 Secondary-Sphere Design in Organometallic Catalysis3 Secondary-Sphere Modification in Organocatalysis4 Using Statistical Analysis to Systematically Tune and Probe Secondary-Sphere Interactions5 Conclusion

Relation of Selective Oxidation Catalytic Performance to Microenvironment of TiIV Active Site Based on Isotopic Labeling

The microenvironment of active sites in zeolite framework is critical for catalytic performance. Four Ti-MWW titanosilicates, prepared by different methods in this study, fell into two categories i...

Mimicking peroxidase active site microenvironment by functionalized graphene quantum dots

The development of high-efficiency peroxidase mimetics is highly desirable in view of high cost and low stability of natural enzymes. From the perspective of mimicking active site microenvironment at low cost, we herein report a novel histidine-functionalized graphene quantum dot (His-GQD)/hemin complex, which exhibits the highest catalytic rate for the peroxidase-based chromogenic reaction among the hemin-containing mimetics reported so far. Also, our peroxidase mimetic shows excellent tolerance to strongly acidic conditions and can function in a wide temperature range. Lineweaver-Burk plots and comprehensive electron paramagnetic resonance analysis reveal a ping-pong type catalytic mechanism for this mimetic. In addition, His-GQD/hemin demonstrates high efficiency and accuracy in detecting H2O2 and blood glucose. Our work provides an effective design of artificial enzymes for practical applications.

Enhanced Thermostability and Anticancer Activity in Breast Cancer Cells of Laccase Immobilized on Pluronic-Stabilized Nanoparticles.

Laccases are multi-copper oxidase enzymes having widespread applications in various biotechnological fields. However, low stability of free enzymes restricts their industrial use. Development of effective methods to preserve and even increase the enzymatic activity is critical to maximize their use, though this remains a challenge. In the present study we immobilized Trametes versicolor laccase on pH-responsive (and charge-switchable) Pluronic-stabilized silver nanoparticles (AgNPsTrp). Our results demonstrate that colloidal stabilization of AgNPsTrp with the amphiphilic copolymer Pluronic F127 enhances enzyme activity (AgNPsTrpF1 + Lac6) by changing the active site microenvironment, which is confirmed by circular dichroism (CD) and fluorescence spectroscopy. Detailed kinetic and thermodynamic studies reveal a facile strategy to improve the protein quality by lowering the activation energy and expanding the temperature window for substrate hydrolysis. The immobilized nanocomposite did not show any change in flow behavior which indirectly suggests that the enzyme stability is maintained, and the enzyme did not aggregate or unfold upon immobilization. Finally, assessing the anticancer efficacy of this nanocomposite in breast cancer MCF-7 cells shows the inhibition of cell proliferation through β-estradiol degradation and cells apoptosis. To understand the molecular mechanism involved in this process, semi qRT-PCR experiments were performed, which indicated significant decrease in the mRNA levels of anti-apoptotic genes, for example, BCL-2 and NF-kβ, and increase in the mRNA level of pro-apoptotic genes like p53 in treated cells, compared to control. Overall, this study offers a completely new strategy for tailoring nano-bio-interfaces with improved activity and stability of laccase.

Structural insights into the mechanism of internal aldimine formation and catalytic loop dynamics in an archaeal Group II decarboxylase

Formation of the internal aldimine (LLP) is the first regulatory step that activates pyridoxal 5′-phosphate (PLP) dependent enzymes. The process involves a nucleophilic attack on PLP by an active site Lys residue, followed by proton transfers resulting in a carbinolamine (CBA) intermediate that undergoes dehydration to form the aldimine. Despite a general understanding of the pathway, the structural basis of the mechanistic roles of specific residues in each of these steps is unclear. Here we determined the crystal structure of the LLP form (holo-form) of a Group II PLP-dependent decarboxylase from Methanocaldococcus jannaschii (MjDC) at 1.7 Å resolution. By comparing the crystal structure of MjDC in the LLP form with that of the pyridoxal-P (non-covalently bound aldehyde) form, we demonstrate structural evidence for a water-mediated mechanism of LLP formation. A conserved extended hydrogen-bonding network around PLP coupled to the pyridinyl nitrogen influences activation and catalysis by affecting the electronic configuration of PLP. Furthermore, the two cofactor bound forms revealed open and closed conformations of the catalytic loop (CL) in the absence of a ligand, supporting a hypothesis for a regulatory link between LLP formation and CL dynamics. The evidence suggests that activation of Group II decarboxylases involves a complex interplay of interactions between the electronic states of PLP, the active site micro-environment and CL dynamics.

Structural and Biochemical Insights into the Reactivity of Thioredoxin h1 from Chlamydomonas reinhardtii.

Thioredoxins (TRXs) are major protein disulfide reductases of the cell. Their redox activity relies on a conserved Trp-Cys-(Gly/Pro)-Pro-Cys active site bearing two cysteine (Cys) residues that can be found either as free thiols (reduced TRXs) or linked together by a disulfide bond (oxidized TRXs) during the catalytic cycle. Their reactivity is crucial for TRX activity, and depends on the active site microenvironment. Here, we solved and compared the 3D structure of reduced and oxidized TRX h1 from Chlamydomonas reinhardtii (CrTRXh1). The three-dimensional structure was also determined for mutants of each active site Cys. Structural alignments of CrTRXh1 with other structurally solved plant TRXs showed a common spatial fold, despite the low sequence identity. Structural analyses of CrTRXh1 revealed that the protein adopts an identical conformation independently from its redox state. Treatment with iodoacetamide (IAM), a Cys alkylating agent, resulted in a rapid and pH-dependent inactivation of CrTRXh1. Starting from fully reduced CrTRXh1, we determined the acid dissociation constant (pKa) of each active site Cys by Matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) mass spectrometry analyses coupled to differential IAM-based alkylation. Based on the diversity of catalytic Cys deprotonation states, the mechanisms and structural features underlying disulfide redox activity are discussed.

Structural insights into the catalytic mechanism of 5-methylthioribose 1-phosphate isomerase

5-Methylthioribose 1-phosphate isomerase (M1Pi) is a crucial enzyme involved in the universally conserved methionine salvage pathway (MSP) where it is known to catalyze the conversion of 5-methylthioribose 1-phosphate (MTR-1-P) to 5-methylthioribulose 1-phosphate (MTRu-1-P) via a mechanism which remains unspecified till date. Furthermore, although M1Pi has a discrete function, it surprisingly shares high structural similarity with two functionally non-related proteins such as ribose-1,5-bisphosphate isomerase (R15Pi) and the regulatory subunits of eukaryotic translation initiation factor 2B (eIF2B). To identify the distinct structural features that lead to divergent functional obligations of M1Pi as well as to understand the mechanism of enzyme catalysis, the crystal structure of M1Pi from a hyperthermophilic archaeon Pyrococcus horikoshii OT3 was determined. A meticulous structural investigation of the dimeric M1Pi revealed the presence of an N-terminal extension and a hydrophobic patch absent in R15Pi and the regulatory α-subunit of eIF2B. Furthermore, unlike R15Pi in which a kink formation is observed in one of the helices, the domain movement of M1Pi is distinguished by a forward shift in a loop covering the active-site pocket. All these structural attributes contribute towards a hydrophobic microenvironment in the vicinity of the active site of the enzyme making it favorable for the reaction mechanism to commence. Thus, a hydrophobic active-site microenvironment in addition to the availability of optimal amino-acid residues surrounding the catalytic residues in M1Pi led us to propose its probable reaction mechanism via a cis-phosphoenolate intermediate formation.

Amino acid function relates to its embedded protein microenvironment: A study on disulfide-bridged cystine.

In our previous study, we have shown that the microenvironments around conserved amino acids are also conserved in protein families (Bandyopadhyay and Mehler, Proteins 2008; 72:646-659). In this study, we have hypothesized that amino acids perform similar functions when embedded in a certain type of protein microenvironment. We have tested this hypothesis on the microenvironments around disulfide-bridged cysteines from high-resolution protein crystal structures. Although such cystines mainly play structural role in proteins, in certain enzymes they participate in catalysis and redox reactions. We have performed and report a functional annotation of enzymatically active cystines to their respective microenvironments. Three protein microenvironment clusters were identified: (i) buried-hydrophobic, (ii) exposed-hydrophilic, and (iii) buried-hydrophilic. The buried-hydrophobic cluster encompasses a small group of 22 redox-active cystines, mostly in alpha-helical conformations in a -C-x-x-C- motif from the Oxido-reductase enzyme class. All these cystines have high strain energy and near identical microenvironments. Most of the active cystines in hydrolase enzyme class belong to buried hydrophilic microenvironment cluster. In total there are 34 half-cystines detected in buried hydrophilic cluster from hydrolases, as a part of enzyme active site. Even within the buried hydrophilic cluster, there is clear separation of active half-cystines between surface exposed part of the protein and protein interior. Half-cystines toward the surface exposed region are higher in number compared to those in protein interior. Apart from cystines at the active sites of the enzymes, many more half-cystines were detected in buried hydrophilic cluster those are part of the microenvironment of enzyme active sites. However, no active half-cystines were detected in extremely hydrophilic microenvironment cluster, that is, exposed hydrophilic cluster, indicating that total exposure of cystine toward the solvent is not favored for enzymatic reactions. Although half-cystines in exposed-hydrophilic clusters occasionally stabilize enzyme active sites, as a part of their microenvironments. Analysis performed in this work revealed that cystines as a part of active sites in specific enzyme families or folds share very similar protein microenvironment regions, despite of their dissimilarity in protein sequences and position specific sequence conservations. Proteins 2016; 84:1576-1589. © 2016 Wiley Periodicals, Inc.