Search Results (106)

Perillyl alcohol, a rare monoterpenoid, can be widely used in chemical, agriculture, and food industries and shows promise in medicine as an anticancer agent. The artificial synthesis of perillyl alcohol from β-pinene epoxide using inexpensive and abundant turpentine is chosen for improving its pharmaceutical and industrial applications. This work presents a green and sustainable catalytic process for the rearrangement of β-pinene epoxide to perillyl alcohol. A novel ammonium phosphomolybdate solid acid (AC-COIMI-NH₄PMo) was built via phosphomolybdic acid chemisorption onto an N-basylous site of imidazolized activated carbon followed by ammonia fumigation, which exhibits outstanding catalytic performance in the rearrangement of β-pinene epoxide to perillyl alcohol in nitromethane under mild conditions. At 80 °C over 80 min, nearly complete conversion of the epoxide is achieved with a perillyl alcohol selectivity of 77.3%. Moreover, the used catalyst can be readily recycled after washing with hot nitromethane. The favorable proton-donating capacity of nitromethane for the rearrangement and the comparison of adsorption energies between substrates and main products on ammonium phosphomolybdate are revealed through DFT calculation. Kinetic analysis based on the Langmuir adsorption model indicates that the surface reaction of strongly adsorbed β-pinene epoxide is a rate-determining step and follows a zero-order reaction process; the activation energy is 29.64 kJ/mol within the temperature range of 50–80 °C. Finally, a parallel catalytic rearrangement mechanism is proposed, and an eight-step reaction pathway toward perillyl alcohol is elaborated for β-pinene epoxide conversion on AC-COIMI-NH₄PMo. Full article

RelA/SpoT homologue family enzymes participate in controlling the cellular levels of the alarmone (p)ppGpp, thereby activating the stringent response and promoting survival under stress conditions. These proteins contain an N-terminal catalytic domain and a C-terminal regulatory domain. They catalyze both the synthesis of ppGpp/pppGpp from ATP and GDP/GTP and their hydrolysis to GDP/GTP and pyrophosphate. Here, we report the crystal structure of the N-terminal domain of Rel from Streptococcus equisimilis in complex with pppGpp at 3.2 Å resolution. The asymmetric unit contains a dimer with asymmetric ligation: pppGpp occupies only the synthetase site in one monomer, whereas in the other monomer, it is bound in both the hydrolase and synthetase sites. The two monomers exhibit distinct conformational states, with pronounced rearrangements of the flexible loops surrounding the binding pockets, including the α2/α3 and α8/α9 loops that act as steric gates. Molecular dynamics simulations support the dual binding arrangement and reveal additional probable transient binding sites, including a region in the linker between hydrolase and synthetase subdomains. These findings provide a structural framework for understanding how pppGpp binding modulates the opposing catalytic activities of bifunctional Rel enzymes and suggest possible mechanisms for (p)ppGpp-mediated autoregulation. Full article

Carnitine plays an essential role in fatty acid metabolism, and its biosynthesis is tightly regulated by γ-butyrobetaine hydroxylase (BBOX), an Fe(II)/α-ketoglutarate-dependent dioxygenase. BBOX is the target of mildronate (THP), a clinically used drug for treating ischemic heart diseases. However, the detailed mechanisms of BBOX-catalyzed hydroxylation and the atypical oxidative rearrangement underlying THP inhibition remain elusive. In this study, we employed combined quantum mechanics/molecular mechanics (QM/MM) methods to systematically elucidate these mechanisms at the atomic level. Our calculations reveal that the hydroxylation of γBB proceeds via a classical three-step mechanism in the quintet state, with hydrogen atom abstraction as the rate-determining step. Remarkably, substitution of the C4 methylene group in γBB with an amino group in THP redirects the reaction pathway, as the lone pair electrons on the adjacent nitrogen atom render N-N bond cleavage kinetically favored over hydroxyl rebound, thereby blocking carnitine synthesis. Through systematic evaluation of possible rearrangement pathways, we rule out the previously proposed direct 1,2-H migration and suggest a revised mechanism featuring imine-mediated hydrogen transfer, hydroxyl rebound preceding C-C bond formation, and final radical coupling. This work provides a detailed atomic-level understanding of both the catalytic and inhibitory mechanisms of BBOX, revealing how substrate electronic effects dictate reaction outcomes. The elucidated mechanistic insights offer a theoretical foundation for understanding the catalytic versatility of the αKG-dependent dioxygenase family and provide valuable guidance for the rational design of novel BBOX inhibitors. Full article

Lauric acid is a characteristic component of Litsea cubeba seed oil, but FatB thioesterase candidates with predicted structural compatibility for C12 acyl-substrate accommodation remain insufficiently defined. In this study, seed oil content and fatty acid composition were examined during L. cubeba seed development. The fatty acid profile shifted from a C18:2-rich pattern at the early stage to a C12:0-dominated composition at later stages, providing the biochemical context for FatB candidate prioritization. Three FatB-like candidates were retrieved from a de novo seed transcriptome assembly and named LcFatB1, LcFatB2, and LcFatB3. Phylogenetic analysis, conserved motif comparison, sequence alignment, and homology modeling showed that LcFatB1 and LcFatB2 retained more complete FatB-like sequence and structural features than LcFatB3. S-dodecanoyl-4′-phosphopantetheine was used as a C12 acyl-4′-phosphopantetheine surrogate for molecular docking. Docking analysis indicated that LcFatB1 and LcFatB2 formed more interpretable C12-bound poses than LcFatB3. Subsequent 150 ns molecular dynamics simulations, free energy landscape analysis, residue–ligand interaction profiling, and catalytic tunnel analysis further distinguished the two main candidates. Compared with LcFatB2, LcFatB1 maintained a lower-displacement C12-bound state, a more compact contact environment involving Tyr116, Ser125, and Asn278, and a main tunnel with higher throughput and shorter length in the representative global-minimum conformation. LcFatB2 also retained the C12 surrogate but stabilized it in a distinct rearranged binding environment. These results support LcFatB1 as the strongest structurally prioritized FatB candidate among the three transcriptome-derived proteins, while LcFatB2 remains a plausible FatB-like candidate with a distinct C12-bound state. This prioritization provides computational structural clues for future biochemical testing but should not be interpreted as direct functional confirmation of FatB activity in vivo. Full article

The cleavage of cumene hydroperoxide (CHP) via the Hock rearrangement is a cornerstone process in the chemical industry, responsible for over 90% of global phenol and acetone production. Despite its industrial significance, the conventional use of homogeneous sulfuric acid catalysis presents critical drawbacks, including severe equipment corrosion, generation of hazardous waste, and the need for complex neutralization steps. This review explores the transition toward heterogeneous solid acid catalysts as a sustainable alternative, emphasizing the relationship between catalyst structure, surface acidity, and reaction performance. Key catalyst families—such as ion-exchange resins, zeolites, and heteropolyacids—are systematically evaluated, with a focus on how Brønsted acid site density and porous architecture influence catalytic activity and selectivity. Particular attention is given to deactivation mechanisms, including coking, leaching of active species, and poisoning by inorganic cations, alongside mitigation strategies enabled by rational catalyst design and regeneration protocols. Additionally, we highlight recent progress in reactor engineering, particularly the integration of solid acid catalysts in reactive distillation and microchannel configurations. These insights offer a strategic perspective for developing more efficient and environmentally benign industrial processes for the Hock cleavage of cumene hydroperoxide. Full article

Lignin, a complex and heterogeneous polymer, poses significant challenges for effective thermal valorization due to its broad molecular weight distribution and structural diversity. This study systematically compares the effect of lignin’s molecular weight on product distribution under pyrolysis and Ru/C-catalyzed depolymerization conditions. Fractionated lignin samples with distinct molecular weights were subjected to identical thermal and catalytic conversion pathways. Pyrolysis results indicate that, compared with low-molecular-weight (low-MW) lignin, high-molecular-weight (high-MW) lignin more readily generates phenolic compounds, with the relative content of guaiacol increasing by nearly twofold. In contrast, products derived from low-MW lignin contain a higher abundance of unsaturated structures, such as 4-allyl-2,6-dimethoxyphenol, suggesting that side chain cleavage and rearrangement reactions are more pronounced. In contrast, Ru/C-catalyzed depolymerization exhibits a stronger molecular-weight-dependent selectivity, where low-MW lignin is more readily converted into carboxylic acids due to enhanced accessibility of terminal functional groups and reduced structural condensation. This comparative analysis demonstrates that lignin’s molecular weight plays a process-dependent role in governing product distribution, providing guidance for tailored lignin valorization strategies. Full article

Polyethylene terephthalate (PET) is a synthetic polymer that is widely used in the production of textiles, packaging materials, and beverage bottles. However, its high durability and resistance to abiotic degradation result in serious environmental and health problems. PETase is an enzyme that can depolymerize PET into value-added products, thereby providing an environmentally friendly strategy for PET recycling. PETaseSM14 from a marine sponge, Streptomyces sp. SM14, has a high salt tolerance and thermal stability, thus suggesting its potential for PET degradation applications. However, the substrate recognition mechanism of PETase remains unclear because the catalytic residue is buried within residues that form the substrate-binding cleft. To elucidate the molecular mechanism of PETaseSM14, all-atom molecular dynamics simulations were performed at 300, 320, and 340 K. The results revealed that the overall α/β fold remained stable at all temperatures, whereas temperature-dependent local fluctuations and conformational changes were observed in the substrate-binding cleft and N-terminal region. At 300 and 320 K, positional shifts and conformational changes in Tyr88 exposed the catalytic Ser156 to the solvent, thereby forming a potential substrate-binding cleft. In contrast, at 340 K, which is higher than the melting temperature of PETaseSM14, disruption of the charge-relay system of the catalytic triad occurs through conformational changes in His234. Substantial temperature-dependent conformational and positional changes in the N-terminal region of PETaseSM14 were observed at 320 and 340 K. These results provide mechanistic insight into the temperature-dependent active-site rearrangements and offer rational engineering strategies to enhance the efficiency of PETase for PET biodegradation. Full article

Nme1Cas9 is an encouraging genome-editing tool with high fidelity and compactness, but its applications are limited by poor catalytic efficiency compared with SpyCas9. Understanding the dynamic activation mechanism of the HNH nuclease domain is the key to breaking the kinetic bottleneck. Here, we integrated Steered Molecular Dynamics (SMD) with the Traveling-Salesman-based automated Path Searching (TAPS) algorithm to reconstruct the atomic-level activation landscape of the L1-HNH module. The simulations suggest a complex “Lifting-Rearrangement-Sliding” pathway, revealing the critical role of a “Backbone Sliding” conformation; in this step, the HNH domain rotates across the R-loop surface. A thermodynamic analysis using free energy decomposition by MM/PBSA indicates that the intrinsic instability of the wild-type HNH/R-loop interface constitutes the predominant energetic barrier. Hyperactive variants (S593Q/W596K and S593Q/W596R) can overcome this barrier by substantially increasing binding affinity to the R-loop through a “Geometry–Electrostatics Synergism”: S593Q improves interfacial proximity, whereas W596K/R acts as an “Electrostatic Anchor.” The results of unbiased MD simulations demonstrate that strengthened interfacial interactions effectively promote spontaneous conformational drift toward the activated state. This computational study proposes a novel in silico model for “Dynamic Interface Engineering” in which reinforcing transient interfacial contacts during conformational sliding can be an effective strategy in developing high-efficiency CRISPR-Cas effectors. Full article

The influence of potassium oxide (K₂O) doping on the hydrodeoxygenation (HDO) performance of trimetallic CoMo–Ni/Al₂O₃ catalysts was systematically investigated using guaiacol as a lignin-derived model compound. Catalysts containing 0, 1, 3, and 5 wt% K₂O were synthesized and characterized by SEM-EDS, N₂ physisorption, XRD, FTIR, and HRTEM. SEM micrographs showed homogeneous morphologies with no significant agglomeration, while EDS analysis confirmed elemental compositions close to nominal values, with K₂O contents increasing proportionally and maintaining uniform surface distribution. Adsorption–desorption isotherms confirmed mesoporous structures with specific surface areas ranging from 258 to 184 m² g⁻¹, decreasing with increasing K₂O loading. XRD revealed γ-Al₂O₃, NiO, (NH₄)₃[CoMo₆O₂₄H₆]·7H₂O, and K₂O phases, with slight peak shifts indicating surface modification rather than lattice incorporation of K⁺. FTIR spectra evidenced characteristic polyoxomolybdate vibrations and metal–oxygen interactions with alumina. HRTEM revealed MoS₂ slab lengths between 1.85 and 2.51 nm, stacking numbers from 2.08 to 3.17, and Mo edge-to-corner ratios (f_e/fc) between 1.39 and 2.43, corresponding to dispersions of 0.45–0.57. Guaiacol conversion remained high (≥95%) for all catalysts, while HDO selectivity strongly depended on K₂O content. At 5 wt% K₂O, cyclohexane selectivity reached 81.3% with an HDO degree of 65%, compared to 52.0% and 31% for the undoped catalyst. Pseudo-first-order kinetic analysis revealed that potassium promotes demethylation and demethoxylation steps while suppressing rearrangement pathways, steering the reaction network toward direct deoxygenation. These results demonstrate that K₂O acts as an efficient structural and electronic promoter, enabling precise control of HDO selectivity without compromising catalytic activity. Full article

Catalytic oxidation has proven to be an effective method for treating low-concentration ventilation air methane. However, regenerative catalytic oxidizers (RCOs) used for ventilation air methane (VAM) treatment often face engineering challenges such as low oxidation efficiency and uneven heat transfer, which limit their overall performance and reliability. This study proposes a CFD-based structural optimization approach that couples flow field, temperature field, concentration field, and chemical reaction processes to systematically analyze the heat transfer and reaction mechanisms within the RCO. The key operational parameters of the reaction process were further discussed. The research focuses on improving temperature uniformity and enhancing methane conversion efficiency to achieve superior thermal efficiency and more effective methane mitigation. The results show that increasing the number of the electric heating rods and rearranging their configuration improved the temperature uniformity of the catalyst layer by 0.2842 (from 0.5462 to 0.8304). Additionally, the installation of a flow distribution plate further enhanced temperature uniformity by 0.1481 (from 0.8304 to 0.9785). As a result of these structural optimizations, the methane conversion rate of the new system increased significantly from 65% to 95%. This study offers valuable insights for future RCO design and optimization, paving the way for more efficient and reliable VAM treatment technologies. Full article

ABO₃ perovskite oxides are a versatile class of materials whose surfaces and interfaces play essential roles in sustainable energy technologies, including catalysis, solid oxide fuel and electrolysis cells, thermoelectrics, and energy-relevant oxide electronics. The interplay between point defects and surface reconstructions strongly affects interfacial stability, charge transport, and catalytic activity under operating conditions. This review summarizes recent progress in understanding how oxygen vacancies, cation nonstoichiometry, and electronic defects couple to atomic-scale surface rearrangements in representative perovskite systems. We first revisit Tasker’s classification of ionic surfaces and clarify how defect chemistry provides compensation mechanisms that stabilize otherwise polar or metastable terminations. We then discuss experimental and theoretical insights into defect-mediated reconstructions on perovskite surfaces and how they influence the performance of energy conversion devices. Finally, we conclude with a perspective on design strategies that leverage defect engineering and surface control to enhance functionality in energy applications, aiming to connect fundamental surface science with practical materials solutions for the transition to sustainable energy. Full article

Ferrocenium catalysis is a growing field of research. This study investigates the catalytic activity of different ferrocenium salts in propargylic substitution reactions to afford propargylic ethers. Four different ferrocenium catalysts were employed in the title reaction, which was monitored over time. The rate of the disappearance of the starting material can be fitted to a first order rate law and observed rate constants were determined. The catalyzed propargylic substitution reactions display a moderate but discernible dependence on the ferrocenium counterion. The lack of an induction period for the reaction indicates that the ferrocenium cation itself is catalytically active, and not just a decomposition product thereof, which would result in an induction period. The presence of a carboxylic acid substituent on one of the cyclopentadienyl rings enhances catalytic activity. The Meyer–Schuster rearrangement of the propargylic alcohol to the corresponding conjugated enone played only a minor role in the ferrocenium-catalyzed reactions. Catalyst decomposition moderately retards the reaction but does not suppress product formation, as demonstrated by experiments with aged FcBF₄. In contrast, the presence of TEMPO as a radical scavenger completely inhibits product formation, while not causing detectable catalyst decomposition at room temperature. In turn, FeCl₃ catalyzes both the propargylic substitution and the Meyer–Schuster rearrangement equally and decomposes the catalysis product over time. These findings reinforce the notion that strong Lewis acids readily promote the rearrangement of propargylic alcohols and that Lewis acidity plays a crucial role in finding a balance between the substitution reactions of propargylic alcohols and their rearrangement to unsaturated aldehydes. Full article

Nitrate (NO₃⁻), as a stable nitrogen-containing compound, has caused serious harm to the ecological environment and human health. To reduce nitrate pollution, the catalytic reduction of nitrate (NO₃RR) to ammonia (NH₃) is a very promising solution. Recently, single-atom catalysts (SACs) have received extensive attention due to their excellent activity and stability. Here, we study the nitrate catalytic reduction properties of hexagonal-boron-nitride-(h-BN)-supported single-atom Cu systematically and theoretically and compare it with monolayer h-BN. We find that (1) due to the stronger electronegativity of the N atom, Cu atom is preferentially doped at the N top site, resulting in the significant electron rearrangement; (2) the doped Cu atom at the N top site for monolayer h-BN can provide extra 3d-orbital electrons at the Fermi level, which can significantly enhance the conductivity, reduce the bandgap width, and increase the reducibility; (3) the NO₃⁻ ion preferentially adsorbs at the hollow site of monolayer h-BN, while the NO₃⁻ ion is adsorbed more strongly at the Cu top site of h-BN-supported single-atom Cu due to the abundant d-electron supply from the Cu atom; (4) single-atom Cu can significantly reduce the energy barrier of the rate-determining step (RDS) and increase the probability of nitrate reduction. In conclusion, h-BN-supported single-atom Cu exhibits excellent catalytic performance of NO₃RR. Full article

Phosphoric acid (H₃PO₄) pretreatment is an effective method to improve biochar properties, yet its evolution mechanism remains incompletely elucidated. This study investigated the synergistic pyrolysis of H₃PO₄ and mottled bamboo at different temperatures in a fixed-bed reactor. Results showed that during impregnation, H₃PO₄ promoted the partial dissolution of hemicellulose and reduced cellulose polymerization, resulting in a decrease in the activation energy of the fast pyrolysis stage from 96.72 kJ/mol (pristine bamboo biochar, MB) to 75.75 kJ/mol (H₃PO₄-modified bamboo biochar, MB/H₃PO₄). With increasing temperature, the pore structure of the modified biochar was enhanced while its graphitization degree decreased, owing to the catalytic effect of H⁺ and the cross-linking action of the acid. Meanwhile, the addition of H₃PO₄ facilitated the rearrangement of oxygen-containing heterocycles, and the incorporation of small-molecule benzene rings further improved the aromatization degree of the modified biochar. In conclusion, it functions as a catalyst, reactant, and pore-expanding agent during pyrolysis. This study further broadens the understanding of biochar evolution mechanisms regulated by phosphorus-containing additives, and provides a theoretical basis for optimizing biochar properties and producing phosphorus-rich biochar. Full article

Pre-mRNA splicing is catalyzed by the ribonucleoprotein (RNP) complex known as the spliceosome. The spliceosomes are dynamic and undergo constant rearrangement, leading to the formation of the different spliceosomal complexes A, B, B^act, C, C*, and P. Isolation of the spliceosomal complex at a specific intermediate stage requires a means to enrich it. This study describes a strategy for studying intermediate spliceosomal complexes by combining BioID with splicing assays. The MINX splicing substrate with a mutation at the 3′ splice site was utilized to arrest and capture the spliceosomal C* complex before the second catalytic step of splicing. The splicing substrate also contains binding sites for the MS2 coat protein, which facilitates the pull-down of assembled complex by FLAG-MS2-tagged RNP immunoprecipitation and determines the captured proximal proteins by mass spectrometry. Full article