Adsorption Site Regulation to Guide Atomic Design of Ni–Ga Catalysts for Acetylene Semi‐Hydrogenation

Atomic regulation of metal catalysts has emerged as an intriguing yet challenging strategy to boost product selectivity. Here, we report a density functional theory‐guided atomic design strategy for the fabrication of a NiGa intermetallic catalyst with completely isolated Ni sites to optimize acetylene semi‐hydrogenation processes. Such Ni sites show not only preferential acetylene π‐adsorption, but also enhanced ethylene desorption. The characteristics of the Ni sites are confirmed by multiple characterization techniques, including aberration‐corrected high‐resolution scanning transmission electron microscopy and X‐ray absorption spectrometry measurements. The superior performance is also confirmed experimentally against a Ni₅Ga₃ intermetallic catalyst with partially isolated Ni sites and against a Ni catalyst with multi‐atomic ensemble Ni sites. Accordingly, the NiGa intermetallic catalyst with the completely isolated Ni sites shows significantly enhanced selectivity to ethylene and suppressed coke formation.     

Direct Estimation of the Surface Location of Immobilized Functional Groups for Concerted Catalysis Using a Probe Molecule

The location of active sites during concerted catalysis by a metal complex and tertiary amine on a SiO₂ surface is discussed based on the interaction between the functionalized SiO₂ surface and a probe molecule, p‐formyl phenylboronic acid. The interactions of the probe molecule with the surface functionalities, diamine ligand, and tertiary amine, were analyzed by FT‐IR and solid‐state ¹³C and ¹¹B MAS NMR. For the catalyst exhibiting high 1,4‐addition activity, the diamine ligand and tertiary amine base exist in closer proximity than in the catalyst with low activity.     

Visible-Light-Induced Heptacene Generation under Ambient Conditions: Utilization of Single-crystal Interior as an Isolated Reaction Site

The photo-induced generation of unstable molecules generally requires stringent conditions to prevent oxidation and the concomitant decomposition of the products. The visible-light-induced conversion of two heptacene precursors to heptacene was studied. Single crystals of bis- and mono-α-diketone-type heptacene precursors ( 7-DK2 and 7-DK1 , respectively), were prepared to investigate the effect of precursor structure on reactivity. The photoirradiation of a 7-DK2 single crystal cleaved only one α-diketone group, forming an intermediate bearing a pentacene subunit, while that of a 7-DK1 single crystal gave rise to characteristic absorption peaks of heptacene and their increase in intensity with photoirradiation time, indicating the generation of heptacene without decomposition. Heptacene production was not observed when the precursors were photoirradiated in solution, implying that the single crystal interior provided isolation from the external environment, thus preventing heptacene oxidation.     

Non‐Oxidative Methane Conversion Using Lead‐ and Iron‐Modified Albite Catalysts in Fixed‐Bed Reactor

Raw and modified albite catalysts, including Pb/Albite and Fe/Albite catalysts, have been investigated for methane conversion to C₂ hydrocarbons under non‐oxidative conditions. Introduction of Pb to albite improved the activity and selectivity to non‐coke products. Based on characterization, it was found that Pb entered into the alkali and alkaline‐earth metal sites of albite, while partial Fe doped in the tetrahedron sites and the other loaded on the surface of albite. At the reaction temperature of 1073 K, methane gas hourly space velocity (GHSV) of 2 L·gcat^–1·h^–1, catalyst dosage of 0.25 g (300 mesh), the methane conversion catalyzed by raw albite in the fixed‐bed micro reactor exhibited a methane conversion of 3.32%. Notably, introducing a Pb content of 3.4 wt% into albite greatly enhanced the conversion of methane up to 8.19%, and the selectivity of C₂ hydrocarbons reached 99% without any coke under the same reaction conditions. While Fe‐doping could weakly heighten the methane conversion to 3.97%, and coke was formed. Thus, a comparison of Pb/Albite and Fe/Albite catalysts demonstrates that the catalytic activity of albite is mainly decided by alkali and alkaline‐earth metal sites, and lead‐modification can effectively improve the catalytic activity of albite.     

Prediction of the interaction of metallic moieties with proteins: An update for protein‐ligand docking techniques

In this article, we present a new approach to expand the range of application of protein‐ligand docking methods in the prediction of the interaction of coordination complexes (i.e., metallodrugs, natural and artificial cofactors, etc.) with proteins. To do so, we assume that, from a pure computational point of view, hydrogen bond functions could be an adequate model for the coordination bonds as both share directionality and polarity aspects. In this model, docking of metalloligands can be performed without using any geometrical constraints or energy restraints. The hard work consists in generating the convenient atom types and scoring functions. To test this approach, we applied our model to 39 high‐quality X‐ray structures with transition and main group metal complexes bound via a unique coordination bond to a protein. This concept was implemented in the protein‐ligand docking program GOLD. The results are in very good agreement with the experimental structures: the percentage for which the RMSD of the simulated pose is smaller than the X‐ray spectra resolution is 92.3% and the mean value of RMSD is < 1.0 Å. Such results also show the viability of the method to predict metal complexes–proteins interactions when the X‐ray structure is not available. This work could be the first step for novel applicability of docking techniques in medicinal and bioinorganic chemistry and appears generalizable enough to be implemented in most protein‐ligand docking programs nowadays available. © 2017 Wiley Periodicals, Inc.     

Revised mechanism of carboxylation of ribulose‐1,5‐biphosphate by rubisco from large scale quantum chemical calculations

Here, we describe a computational approach for studying enzymes that catalyze complex multi‐step reactions and apply it to Ribulose 1,5‐bisphosphate carboxylase–oxygenase (Rubisco), the enzyme that fixes atmospheric carbon dioxide within photosynthesis. In the 5‐step carboxylase reaction, the substrate Ribulose‐1,5‐bisphosphate (RuBP) first binds Rubisco and undergoes enolization before binding the second substrate, CO₂. Hydration of the RuBP.CO₂ complex is followed by C C bond scission and stereospecific protonation. However, details of the roles and protonation states of active‐site residues, and sources of protons and water, remain highly speculative. Large‐scale computations on active‐site models provide a means to better understand this complex chemical mechanism. The computational protocol comprises a combination of hybrid semi‐empirical quantum mechanics and molecular mechanics within constrained molecular dynamics simulations, together with constrained gradient minimization calculations using density functional theory. Alternative pathways for hydration of the RuBP.CO₂ complex and associated active‐site protonation networks and proton and water sources were investigated. The main findings from analysis of the resulting energetics advocate major revision to existing mechanisms such that: hydration takes place anti to the CO₂; both hydration and C C bond scission require early protonation of CO₂ in the RuBP.CO₂ complex; C C bond scission and stereospecific protonation reactions are concerted and, effectively, there is only one stable intermediate, the C3‐gemdiolate complex. Our main conclusions for interpreting enzyme kinetic results are that the gemdiolate may represent the elusive Michaelis–Menten‐like complex corresponding to the empirical K_m (=K_c) with turnover to product via bond scission concerted with stereospecific protonation consistent with the observed catalytic rate. © 2018 Wiley Periodicals, Inc.     

Characterization of complex,heterogeneous lipid A samples using HPLC‐MS/MS technique III. Positive‐ion mode tandem mass spectrometry to reveal phosphorylation and acylation patterns of lipid A

In this study, we report the detailed analysis of the fragmentation patterns of positively charged lipid A species based on their tandem mass spectra obtained under low‐energy collision‐induced dissociation conditions of an electrospray quadrupole time‐of‐flight mass spectrometer. The tandem mass spectrometry experiments were performed after the separation of the compounds with a reversed‐phase high performance liquid chromatography method. We found that both, phosphorylated and nonphosphorylated lipid A molecules can be readily ionized in the positive‐ion mode by adduct formation with triethylamine added to the eluent. The tandem mass spectra of the lipid A triethylammonium adduct ions showed several product ions corresponding to inter‐ring glycosidic cleavages of the sugar residues, as well as consecutive and competitive eliminations of fatty acids, phosphoric acid, and water following the neutral loss of triethylamine. Characteristic product ions provided direct information on the phosphorylation site(s), also when phosphorylation isomers (ie, containing either a C1 or a C4′ phosphate group) were simultaneously present in the sample. Continuous series of high‐abundance B‐type and low‐abundance Y‐type inter‐ring fragment ions were indicative of the fatty acyl distribution between the nonreducing and reducing ends of the lipid A backbone. The previously reported lipid A structures of Proteus morganii O34 and Escherichia coli O111 bacteria were used as standards. Although, the fragmentation pathways of the differently phosphorylated lipid A species significantly differed in the negative‐ion mode, they were very similar in the positive‐ion mode. The complementary use of positive‐ion and negative‐ion mode tandem mass spectrometry was found to be essential for the full structural characterization of the C1‐monophosphorylated lipid A species.     

Synthesis and characterization of a photoaffinity labelling probe based on the structure of the cystic fibrosis drug ivacaftor

Cystic Fibrosis (CF) is a genetic disorder caused by loss-of-function mutations to the gene encoding the cystic fibrosis transmembrane conductance regulator (CFTR) protein. Ivacaftor (1) was the first therapeutic approved for the treatment of CF that is able to restore gating activity to certain CFTR variants although the mechanism of action is poorly understood. Herein we describe the synthesis of a photoaffinity labelling (PAL) probe (2) based on the structure of ivacaftor incorporating a photoreactive diazirine moiety for use in labelling studies designed to identify the binding site for ivacaftor on mutant CFTR. The PAL probe 2 retained potentiation activity, with a potency similar to 1, using a Fluorescent Imaging Plate Reader (FLIPR^®) assay measuring ion conductance potentiation of wild type (Wt)-CFTR. Photolabelling experiments with human serum albumin (HSA) as a model protein have shown that probe 2 can label HSA in a manner consistent with observed and predicted binding.     

Application of micro‐solid‐phase extraction for the on‐site extraction of heterocyclic aromatic amines in seawater

An efficient on‐site extraction technique to determine carcinogenic heterocyclic aromatic amines in seawater has been reported. A micro‐solid‐phase extraction device placed inside a portable battery‐operated pump was used for the on‐site extraction of seawater samples. Before on‐site applications, parameters that influence the extraction efficiency (extraction time, type of sorbent materials, suitable desorption solvent, desorption time, and sample volume) were investigated and optimized in the laboratory. The developed method was then used for the on‐site sampling of heterocyclic aromatic amines determination in seawater samples close to distillation plant. Once the on‐site extraction completed, the small extraction device with the analytes was brought back to the laboratory for analysis using high‐performance liquid chromatography with fluorescence detection. Based on the optimized conditions, the calibration curves were linear over the concentration range of 0.05–20 μg/L with correlation coefficients up to 0.996. The limits of detection were 0.004–0.026 μg/L, and the reproducibility values were between 1.3 and 7.5%. To evaluate the extraction efficiency, a comparison was made with conventional solid‐phase extraction and it was applied to various fortified real seawater samples. The average relative recoveries obtained from the spiked seawater samples varied in the range 79.9–95.2%.     

MTD-ADJ: A multiconformational minimal topologic difference for determining bioactive conformers using adjusted biological activities

The active conformation is part of a conformational mixture with experimental activity Yexp, and is used in QSAR studies to extract more information regarding the ligand-receptor interaction. To reflect the relative amount () of the active conformation, we adjust Yexp : Yadj = Yexp - log . We establish a quantitative structure-activity relationship (QSAR) between Yadj and 3D conformational characteristics for the acetylcholinesterase (AChE) hydrolysis rates of 25 acetic esters. The 3D-QSAR model was obtained using the adjusted multiconformational minimal steric/topologic difference (MTD-ADJ) method, optimizing the receptor map based on Yadj for each conformer. Yadj was updated during each step of the optimization process. and Yadj are based on the Boltzmann distribution calculated using AM1 (MOPAC 6.0) relative energies of the COSMIC 90 derived conformers. The MTD-ADJ results are: (i) the 3D-QSAR models obtained by this procedure have significant statistical parameters and are similar to the unadjusted (MTD-MC, using Yexp) models; (ii) the selected bioactive conformations are extended, occupy cavity vertices and, for the same structures, have the same MTD value; and (iii) the optimized conformational map of the neutral ligands obtained from the MTD-ADJ model fits well in the active site of the crystallographic structure of AChE (from Torpedo californica). We propose a neutral ligands binding site model for AchE. Our results show that MTD-ADJ, which can be implemented in any 3D-QSAR method, is capable of providing additional information regarding the active conformations, and can be used to gain further insight into the ligand-receptor models for which no structural data are available.