Modifying the Reactivity of Single Pd Sites in a Trimetallic Sn-Pd-Ag Surface Alloy: Tuning CO Binding Strength.

Improving control over active-site reactivity is a grand challenge in catalysis. Single-atom alloys (SAAs) consisting of a reactive component doped as single atoms into a more inert host metal feature localized and well-defined active sites, but fine tuning their properties is challenging. Here, a framework is developed for tuning single-atom site reactivity by alloying in an additional inert metal, which this work terms an alloy-host SAA. Specifically, this work creates about 5% Pd single-atom sites in a Pd33Ag67(111) single crystal surface, and then identifies Sn based on computational screening as a suitable third metal to introduce. Subsequent experimental studies show that introducing Sn indeed modifies the electronic structure and chemical reactivity (measured by CO desorption energies) of the Pd sites. The modifications to both the electronic structure and the CO adsorption energies are in close agreement with the calculations. These results indicate that the use of an alloy host environment to modify the reactivity of single-atom sites can allow fine-tuning of catalytic performance and boost resistance against strong-binding adsorbates such as CO.

Enhancing the antioxidant potential of ESIPT-based naringenin flavonoids based on excited state hydrogen bond dynamics: A theoretical study.

Exploring antioxidant potential of flavonoid derivatives after ESIPT process provides a theoretical basis for discovering compounds with higher antioxidant capacity. In this work, employing the density functional theory (DFT) and time-dependent density functional theory (TD-DFT) methods, the antioxidant potential of two citrus-derived naringenin flavonoids after ESIPT process is explored. Based on studies of ESIPT process including IMHB intensity variations, potential energy curves, and transition state, these molecules exist only in enol and keto⁎ forms due to ultra-fast ESIPT. The HOMOs are utilized to explore electron-donating capacity, demonstrating that the molecules in keto⁎ form is stronger than that in enol form. Furthermore, the atomic dipole moment corrected Hirshfeld population (ADCH) and Fukui functions indicate that the sites attacked by the electrophilic free radical of the two molecules in the keto⁎ form are O3 and O5' respectively, and both are more active than in the enol form. Overall, a comprehensive consideration of the ESIPT process and antioxidant potential of flavonoid derivatives will facilitate the exploration and design of substances with higher antioxidant capacity.

Critical Review of Pd-Catalyzed Reduction Process for Treatment of Waterborne Pollutants.

Catalyzed reduction processes have been recognized as important and supplementary technologies for water treatment, with the specific aims of resource recovery, enhancement of bio/chemical-treatability of persistent organic pollutants, and safe handling of oxygenate ions. Palladium (Pd) has been widely used as a catalyst/electrocatalyst in these reduction processes. However, due to the limited reserves and high cost of Pd, it is essential to gain a better understanding of the Pd-catalyzed decontamination process to design affordable and sustainable Pd catalysts. This review provides a systematic summary of recent advances in understanding Pd-catalyzed reductive decontamination processes and designing Pd-based nanocatalysts for the reductive treatment of water-borne pollutants, with special focus on the interactions and transformation mechanisms of pollutant molecules on Pd catalysts at the atomic scale. The discussion begins by examining the adsorption of pollutants onto Pd sites from a thermodynamic viewpoint. This is followed by an explanation of the molecular-level reaction mechanism, demonstrating how electron-donors participate in the reductive transformation of pollutants. Next, the influence of the Pd reactive site structure on catalytic performance is explored. Additionally, the process of Pd-catalyzed reduction in facilitating the oxidation of pollutants is briefly discussed. The longevity of Pd catalysts, a crucial factor in determining their practicality, is also examined. Finally, we argue for increased attention to mechanism study, as well as precise construction of Pd sites under batch synthesis conditions, and the use of Pd-based catalysts/electrocatalysts in the treatment of concentrated pollutants to facilitate resource recovery.

Photodegradation Kinetics and Solvent Effect of New Brominated Flame Retardants (NBFRS) in Liquid Medium.

The photolysis of four typical NBFRs, hexabromobenzene (HBB), pentabromotoluene (PBT), pentabromobenzyl acrylateare (PBBA) and pentabromoethylbenzene (PBEB), were explored under different irradiation light wavelengths, initial concentrations and organic solvents. Density functional theory was used for chemical calculation to explore the internal mechanism of solvent effect. All degradation kinetics conformed to the first-order kinetic model. Under different irradiation light wavelengths, the degradation rates were in the following order: 180~400 nm (0.1702~0.3008 min-1) > 334~365 nm (0.0265~0.0433 min-1) > 400~700 nm (0.0058~0.0099 min-1). When the initial concentration varied from 0.25 mg/L to 1 mg/L, the degradation rate decreased from 0.0379~0.0784 min-1 to 0.0265~0.0433 min-1 under 334~365 nm irradiation, which might be attributed to the reduction in light energy received per unit area and competition from intermediate metabolites. In different organic solvents, the degradation rates were in the order of acetone (0.1702~0.3008 min-1) > toluene (0.0408~0.0534 min-1) > n-hexane (0.0124~0.0299 min-1). Quantum chemical calculation and analysis showed that the energy change in electron transfer between solvent and NBFRs was the key factor to solvent effect in the degradation of NBFRs. The active sites and degradation pathways of NBFRs were also speculated, the nucleophilic reaction of the Br atom on a benzene ring was the main process of photodegradation and it was preferential to remove the bromine and then the ethyl group on the benzene ring. Our research will be helpful in predicting and evaluating their photochemical behavior in different environment conditions.

Unveiling the Role of Sulfur in Rapid Defluorination of Florfenicol by Sulfidized Nanoscale Zero-Valent Iron in Water under Ambient Conditions.

Groundwater contamination by halogenated organic compounds, especially fluorinated ones, threatens freshwater sources globally. Sulfidized nanoscale zero-valent iron (SNZVI), which is demonstrably effective for dechlorination of groundwater contaminants, has not been well explored for defluorination. Here, we show that SNZVI nanoparticles synthesized via a modified post-sulfidation method provide rapid dechlorination (∼1100 µmol m-2 day-1) and relatively fast defluorination (∼6 µmol m-2 day-1) of a halogenated emerging contaminant (florfenicol) under ambient conditions, the fastest rates that have ever been reported for Fe0-based technologies. Batch reactivity experiments, material characterizations, and theoretical calculations indicate that coating S onto the metallic Fe surface provides a highly chemically reactive surface and changes the primary dechlorination pathway from atomic H for nanoscale zero-valent iron (NZVI) to electron transfer for SNZVI. S and Fe sites are responsible for the direct electron transfer and atomic H-mediated reaction, respectively, and ß-elimination is the primary defluorination pathway. Notably, the Cl atoms in florfenicol make the surface more chemically reactive for defluorination, either by increasing florfenicol adsorption or by electronic effects. The defluorination rate by SNZVI is ∼132-222 times higher with chlorine attached compared to the absence of chlorine in the molecule. These mechanistic insights could lead to new SNZVI materials for in situ groundwater remediation of fluorinated contaminants.

Defective binding of SPINK1 variants is an uncommon mechanism for impaired trypsin inhibition in chronic pancreatitis.

The serine protease inhibitor Kazal type 1 (SPINK1) protects the pancreas from intrapancreatic trypsin activation that can lead to pancreatitis. Loss-of-function genetic variants of SPINK1 increase the risk for chronic pancreatitis, often by diminishing inhibitor expression or secretion. Variants that are secreted normally have been presumed to be pathogenic because of defective trypsin inhibition, but evidence has been lacking. Here, we report quantitative studies on the inhibition of human trypsins by wildtype SPINK1 and seven secreted missense variants. We found that tyrosine sulfation of human trypsins weakens binding of SPINK1 because of altered interactions with Tyr43 in the SPINK1 reactive loop. Using authentic sulfated human trypsins, we provide conclusive evidence that SPINK1 variants N34S, N37S, R65Q, and Q68R have unimpaired inhibitory activity, whereas variant P55S exhibits a small and clinically insignificant binding defect. In contrast, rare variants K41N and I42M that affect the reactive-site peptide bond of SPINK1 decrease inhibitor binding by 20,000- to 30,000-fold and three- to sevenfold, respectively. Taken together, the observations indicate that defective trypsin inhibition by SPINK1 variants is an uncommon mechanism in chronic pancreatitis. The results also strengthen the notion that a decline in inhibitor levels explains pancreatitis risk associated with the large majority of SPINK1 variants.

Enzyme annotation for orphan and novel reactions using knowledge of substrate reactive sites.

Thousands of biochemical reactions with characterized activities are "orphan," meaning they cannot be assigned to a specific enzyme, leaving gaps in metabolic pathways. Novel reactions predicted by pathway-generation tools also lack associated sequences, limiting protein engineering applications. Associating orphan and novel reactions with known biochemistry and suggesting enzymes to catalyze them is a daunting problem. We propose the method BridgIT to identify candidate genes and catalyzing proteins for these reactions. This method introduces information about the enzyme binding pocket into reaction-similarity comparisons. BridgIT assesses the similarity of two reactions, one orphan and one well-characterized nonorphan reaction, using their substrate reactive sites, their surrounding structures, and the structures of the generated products to suggest enzymes that catalyze the most-similar nonorphan reactions as candidates for also catalyzing the orphan ones. We performed two large-scale validation studies to test BridgIT predictions against experimental biochemical evidence. For the 234 orphan reactions from the Kyoto Encyclopedia of Genes and Genomes (KEGG) 2011 (a comprehensive enzymatic-reaction database) that became nonorphan in KEGG 2018, BridgIT predicted the exact or a highly related enzyme for 211 of them. Moreover, for 334 of 379 novel reactions in 2014 that were later cataloged in KEGG 2018, BridgIT predicted the exact or highly similar enzymes. BridgIT requires knowledge about only four connecting bonds around the atoms of the reactive sites to correctly annotate proteins for 93% of analyzed enzymatic reactions. Increasing to seven connecting bonds allowed for the accurate identification of a sequence for nearly all known enzymatic reactions.

Structure of a Kunitz-type potato cathepsin D inhibitor.

Potato cathepsin D inhibitor (PDI) is a glycoprotein of 188 amino acids which can inhibit both the aspartic protease cathepsin D and the serine protease trypsin. Here we report the first X-ray structure of PDI at a resolution of 2.1 Å showing that PDI adopts a ß-trefoil fold, which is typical of the Kunitz-family protease inhibitors, with the inhibitory loops protruding from the core. Possible reactive-site loops including one involving a unique disulphide and another involving a protruding 310 helix are identified and docking studies indicate the mode of action of this unusual bi-functional inhibitor.

Surface complexation modeling of Hg(II) adsorption at the goethite/water interface using the charge distribution multi-site complexation (CD-MUSIC) model.

HYPOTHESIS: Previous attempts to describe Hg(II) adsorption onto mineral surfaces using surface complexation models (SCMs) have proven unsuccessful and/or require the use of hypothetical surface species. Given that metal ion adsorption at the mineral-water interface is greatly influenced by mineral surface heterogeneity and the presence of competing adsorbates in solution, it stands to reason that estimating the crystal face composition (CFC) of the mineral surface and the extent of carbonate contamination in the experimental system will improve SCM predictions. EXPERIMENTS: The Charge Distribution Multi-Site Complexation (CD-MUSIC) model was used to simulate experimental Hg(II) adsorption data, collected on the iron hydroxide mineral goethite, in the presence and absence of competing adsorbates and complexing ligands as a function of pH and ionic strength. The CFC of each goethite sample studied was predicted using a newly discovered relationship between goethite's proton reactive site density (N(H)) and specific surface area (SSA). Carbonate's presence in the experimental systems was determined utilizing a novel methodology developed in this work. FINDINGS: The CD-MUSIC model developed in this study accurately predicted Hg(II) adsorption onto goethite over the entire range of experimental conditions investigated while only employing surface species consistent with spectroscopic evidence.

Complementation of intramolecular interactions for structural-functional stability of plant serine proteinase inhibitors.

BACKGROUND: Plant protease inhibitors (PIs) constitute a diverse group of proteins capable of inhibiting proteases. Among PIs, serine PIs (SPIs) display stability and conformational restrictions of the reactive site loop by virtue of their compact size, and by the presence of disulfide bonds, hydrogen bonds, and other weak interactions. SCOPE OF REVIEW: The significance of various intramolecular interactions contributing to protein folding mechanism and their role in overall stability and activity of SPIs is discussed here. Furthermore, we have reviewed the effect of variation or manipulation of these interactions on the activity/stability of SPIs. MAJOR CONCLUSIONS: The selective gain or loss of disulfide bond(s) in SPIs can be associated with their functional differentiation, which is likely to be compensated by non-covalent interactions (hydrogen bonding or electrostatic interactions). Thus, these intramolecular interactions are collectively responsible for the functional activity of SPIs, through the maintenance of scaffold framework, conformational rigidity and shape complementarities of reactive site loop. GENERAL SIGNIFICANCE: Structural insight of these interactions will provide an in-depth understanding of kinetic and thermodynamic parameters involved in the folding and stability mechanisms of SPIs. These features can be explored for engineering canonical SPIs for optimizing their overall stability and functionality for various applications.

Antithrombin deficiency in three Japanese families: one novel and two reported point mutations in the antithrombin gene.

INTRODUCTION: Inherited antithrombin (AT) deficiency is associated with a predisposition to familial venous thromboembolic disease. We analyzed the AT gene in three unrelated patients with an AT deficiency who developed thrombosis. MATERIALS AND METHODS: We analyzed the SERPINC1 gene in three patients. Additionally, we expressed the three mutants in the COS-1 cells and compared their secretion rates and levels of AT activity with those of the wild-type (WT). RESULTS: We identified three distinct heterozygous mutations of c.2534C>T: p.56Arginine → Cysteine (R56C), c.13398C>A: p.459Alanine → Aspartic acid (A459D) and c.2703C>G: p.112 Proline → Arginine (P112R). In the in vitro expression experiments, the AT antigen levels in the conditioned media (CM) of the R56C mutant were nearly equal to those of WT. In contrast, the AT antigen levels in the CM of the A459D and P112R mutants were significantly decreased. The AT activity of R56C was decreased in association with a shorter incubation time in a FXa inhibition assay and a thrombin inhibition-based activity test. However, the AT activity of R56C was comparable to that of WT when the incubation time was increased. CONCLUSIONS: We concluded that the R56C mutant is responsible for type II HBS deficiency. We considered that the A459D and P112R mutants can be classified as belonging to the type I AT deficiency.

The anionic protease inhibitor BWI-1 from buckwheat seeds. Kinetic properties and possible biological role.

Kinetic characteristics and effects on the growth of filamentous fungi of one of the main anionic protease inhibitors, BWI-1, isolated from buckwheat seeds, have been studied. The inhibition constants of bovine trypsin, chymotrypsin and cathepsin G from human granulocytes with BWI-1 were found to be 1.1, 67 and 200 nM, respectively. Analysis of the amino acid sequence of BWI-1 in the vicinity of the reactive site revealed its homology to the potato proteinase inhibitor I family. It is suggested that the inability of BWI-1 to bind elastase of human granulocytes is due to the basic nature of the amino acid residue (Arg) at the Pj position in its reactive site. It was demonstrated that BWI-1 was able to suppress the germination of the spores and the growth of the mycelium of two filamentous fungi.