Oversampling Free Energy Perturbation Simulation in Determination of the Ligand-Binding Free Energy

Determination of the ligand-binding affinity is an extremely interesting problem. Normally, the free energy perturbation (FEP) method provides an appropriate result. However, it is of great interest to improve the accuracy and precision of this method. In this context, temperature replica exchange molecular dynamics implementation of the FEP computational approach, which we call replica exchange free energy perturbation (REP) was proposed. In particular, during REP simulations, the system can easily escape from being trapped in local minima by exchanging configurations with high temperatures, resulting in significant improvement in the accuracy and precision of protein–ligand binding affinity calculations. The distribution of the decoupling free energy was enlarged, and its mean values were decreased. This results in changes in the magnitude of the calculated binding free energies as well as in alteration in the binding mechanism. Moreover, the REP correlation coefficient with respect to experiment ( R^REP = 0.85 ± 0.15 ) is significantly boosted in comparison with the FEP one ( R^FEP = 0.64 ± 0.30 ). Furthermore, the root-mean-square error (RMSE) of REP is also smaller than FEP, RMSE^REP = 4.28 ± 0.69 versus RMSE^FEP = 5.80 ± 1.11 kcal/mol, respectively. © 2019 Wiley Periodicals, Inc.     

Halide Anion Triggered Reactions of Michael Acceptors with Tropylium Ion

Tropylium bromide undergoes noncatalyzed, regioselective additions to a large variety of Michael acceptors. In this way, acrylic esters are converted into β‐bromo‐α‐cycloheptatrienylpropionic esters. The reactions are interpreted as nucleophilic attack of bromide ions at the electron‐deficient olefins and the approach of the tropylium ion to the incipient carbanion. Quantum chemical calculations were performed to elucidate the analogy to the amine‐ or phosphine‐catalyzed Rauhut–Currier reactions. Subsequent synthetic transformations of the bromo‐cycloheptatrienylated adducts are reported.     

An Arylazopyrazole‐Based N‐Heterocyclic Carbene as a Photoswitch on Gold Surfaces: Light‐Switchable Wettability,Work Function,and Conductance

A novel photoresponsive and fully conjugated N‐heterocyclic carbene (NHC) has been synthesized that combines the excellent photophysical properties of arylazopyrazoles (AAPs) with an NHC that acts as a robust surface anchor (AAP‐BIMe). The formation of self‐assembled monolayers (SAMs) on gold was proven by ToF‐SIMS and XPS, and the organic film displayed a very high stability at elevated temperatures. This stability was also reflected in a high desorption energy, which was determined by temperature‐programmed SIMS measurements. E‐/Z‐AAP‐BIMe@Au photoisomerization resulted in reversible alterations of the surface energy (i.e. wettability), the surface potential (i.e. work function), and the conductance (i.e. resistance). The effects could be explained by the difference in the dipole moment of the isomers. Furthermore, sequential application of a dummy ligand by microcontact printing and subsequent backfilling with AAP‐BIMe allowed its patterning on gold. To the best of our knowledge, this is the first example of a photoswitchable NHC on a gold surface. These properties of AAP‐BIMe@Au illustrate its suitability as a molecular switch for electronic devices.     

Triterpene glycosides from the Vietnamese sea cucumber Holothuria edulis

Abstract

From the MeOH extract of the Vietnamese sea cucumber Holothuria edulis, eight triterpene glycosides (1–8), including one new compound namely holothurin A₅ (1), were isolated by using various chromatographic separations. Their structures were established by spectroscopic experiments including 1D, 2D NMR and HR-ESI-MS. Holothurin A₅ (1) has a hydroperoxy group at C-25. To the best of our knowledge, this is the first report of this group in triterpene saponins obtained from sea cucumbers to date. In addition, the in vitro cytotoxicity against five human cancer cell lines (HepG2, KB, LNCaP, MCF7 and SK-Mel2) of all isolated compounds was also evaluated using SRB assays.     

Photoinitiated cationic polymerisation of multifunctional systems

Different types of tridimensional polymer networks have been synthetised by photoinitiated cationic polymerisation of vinyl ether and epoxy-functionalised oligomers and polymers. The polymerisation kinetics was followed by real-time infrared (RTIR) spectroscopy, a technique that records directly conversion versus time profiles in a timescale as short as 1 s. The addition of a diacrylate monomer was shown to accelerate the ring-opening polymerisation of epoxidized polyisoprene, with formation of interpenetrating polymer networks having well contrasted properties. A dual polymer network has been generated by photocrosslinking of a polyisoprene functionalised with both epoxy and acrylate groups.     

Differential effects of various trivalent and pentavalent organic and inorganic arsenic species on glucose metabolism in isolated kidney cells

We have compared the acute toxicities of the trivalent arsenic species arsenite, oxophenylarsine (PhAsO), 2-chlorovinyloxoarsine (ClvinAsO), methyloxoarsine (MeAsO), and of the pentavalent arsenic species arsenate, methyl- and phenyl-arsonic acid in rat kidney tubules (RKT) and Madin-Darby canine kidney (MDCK) cells. In RKT, PhAsO (1 μmol I⁻¹, 60 min) almost completely (>90%) blocked gluconeogenesis without affecting cell viability as assessed by dye exclusion. In MDCK cells, PhAsO (2 μmol I⁻¹) markedly inhibited glucose uptake (60% of controls) within 30 min, while cell viability, as assessed by formazan formation, was not affected within 180 min. MeAsO and CIvinAsO were similarly effective to PhAsO in both RKT and MDCK cells. Estimated IC₅₀ values for the inhibition of gluconeogenesis were 0.55 (PhAsO), 0.69 (CIvinAsO) and 0.99 μmol I⁻¹ (MeAsO) and for the inhibition of glucose uptake 1.23 (PhAsO). 2.62 (CIvinAsO) and 6.99 μmol I⁻¹ (MeAsO). At longer storage times, aqueous solutions of MeAsO and of CIvinAsO, but not of PhAsO, gradually lost toxic activity in RKT and MDCK cells, especially at alkaline pH. Concomitantly, a gradual decrease in content as assessed by HPLC was detected. Roughly 10-fold higher concentrations of arsenite than of PhAsO were required for comparable effects on gluconeogenesis in RKT, whereas in MDCK cells about 100-fold higher concentrations were needed for similar inhibition of glucose uptake. Pentavalent arsenate and phenylarsonate were two orders of magnitude less effective than PhAsO in RKT, while methylarsonate had virtually no influence on gluconeogenic activity. In MDCK cells the pentavalent arsenic species showed effects only in the millimolar range. It is concluded (1) that different mechanisms are involved in the acute toxicity of oxoarsines and inorganic arsenic and (2) that PhAsO offers advantages as a model substance for mono-substituted trivalent arsenicals, because it is more stable and more readily detectable.     

Ring-opening metathesis copolymerization employing ruthenium-based metathesis catalysts

The copolymerization of both high- and low-strain cyclic olefins employing three ruthenium-based metathesis catalysts is desribed. The effect of the ligand environment as well as the nature of the carbene on the copolymerizations is discussed.     

Data assimilation and pollution forecasting in Burgers' equation with model error function

This article presents a correction method for a better resolution of the problem of estimating and predicting pollution, governed by Burgers' equations. The originality of the method consists in the introduction of an error function into the system's equations of state to model uncertainty in the model. The initial conditions and diffusion coefficients, present in the equations for pollution and concentration, and also those in the model error equations, are estimated by solving a data assimilation problem. The efficiency of the correction method is compared with that produced by the traditional method without introduction of an error function.Three test cases are presented in this study in order to compare the performances of the proposed methods. In the first two tests, the reference is the analytical solution and the last test is formulated as part of the “twin experiment”.The numerical results obtained confirm the important role of the model error equation for improving the prediction capability of the system, in terms of both accuracy and speed of convergence.