Challenges of crystal structure prediction of diastereomeric salt pairs

A methodology for the computational prediction of the crystal structures and resolution efficiency for diastereomeric salt pairs is developed by considering the polymorphic system of the diastereomeric salt pair (R)-1-phenylethylammonium (R/S)-2-phenylpropanoate. To alleviate the mathematical complexity of the search for minima in the lattice energy due to the presence of two flexible entities in the asymmetric unit, the range of rigid-body lattice energy global optimizations was guided by a statistical analysis of the Cambridge Structural Database for common ion-pair geometries and ion conformations. A distributed multipole model for the dominant electrostatic interactions and high-level ab initio calculations for the intramolecular energy penalty for conformational distortions are used to quantify the relative stabilities of the p- and n-salt forms. While the ab initio prediction of the known structure of the p-salt as the most stable structure was insensitive to minor changes in the rigid-ion conformations considered, the relative stabilities of the known polymorphs and hypothetical structures of the n-salt were very sensitive. Although this paper provides a significant advance over traditional search algorithms and empirical force fields in determining the structures and relative stabilities of diastereomeric salt pairs, the sensitivity of the computed lattice energies to the fine details of the ion conformations overtaxes current computational models and renders the design of diastereomeric resolution processes by computational chemistry a challenging problem.     

2020 Roadmap on gas-involved photo-and electro-catalysis

In this roadmap, we address the development and perspectives of hydrogen evolution reaction, oxygen reduction reaction, oxygen evolution reaction, carbon dioxide reduction reaction and nitrogen reduction.     

A new protocol for a regioselective aldol condensation as an alternative convenient synthesis of beta-ketols and alpha,beta-unsaturated ketones

A general and convenient synthesis of beta-ketols and alpha,beta-alkenones has been achieved by a Knoevenagel condensation of a beta-ketoacid with an aldehyde in aqueous medium. Saponification of a beta-ketoester by an aqueous KOH 10% solution gives the potassium salt of the beta-ketoacid, which is condensed in situ with an aldehyde at pH 7.8-8.0, at 60 degrees C for 5-6 h. The intermediate beta-ketocarboxylate is smoothly decarboxylated in the reaction medium, giving the beta-ketol in high yield (75-90%). Acidification of the reaction mixture at pH 1 and heating at 70 degrees C under vigorous stirring for 6 h, leads directly to the corresponding alpha,beta-unsaturated ketone in good yield (65-75%).     

Grcarma: A fully automated task‐oriented interface for the analysis of molecular dynamics trajectories

We report the availability of grcarma, a program encoding for a fully automated set of tasks aiming to simplify the analysis of molecular dynamics trajectories of biological macromolecules. It is a cross‐platform, Perl/Tk‐based front‐end to the program carma and is designed to facilitate the needs of the novice as well as those of the expert user, while at the same time maintaining a user‐friendly and intuitive design. Particular emphasis was given to the automation of several tedious tasks, such as extraction of clusters of structures based on dihedral and Cartesian principal component analysis, secondary structure analysis, calculation and display of root‐mean‐square deviation (RMSD) matrices, calculation of entropy, calculation and analysis of variance–covariance matrices, calculation of the fraction of native contacts, etc. The program is free‐open source software available immediately for download. © 2013 Wiley Periodicals, Inc.     

Organic-Inorganic Sol-Gel Hybrids with Ionic Properties

 A hybrid silicon precursor (ICS-PPG) obtained by reaction of 3-isocyanatopropyltriethoxy silane with poly-(propyleneglycol)-bis-(2-aminopropyl ether) was recognized as a potential host for various salts and molecular species. It has been used for electrochromic, gasochromic, photovoltaic, and fuel cell applications. This focuses on proton conducting gels (PWA/ICS-PPG, SiWA/ICS-PPG, and W-PTA/ICS-PPG) obtained after the incorporation of polyoxometalates in the ICS-PPG host. IR spectroscopic measurements are used to reveal the entrapment, the aggregation, and the interactions of W-PTA, PWA, or SiWA with the sol-gel derived network. The proton conductivity of the composites, measured using impedance spectroscopy, increases with increasing concentration of the polyoxometalates from 10⁻⁶ to 10⁻³ S/cm.     

A click-flipped enzyme substrate boosts the performance of the diagnostic screening for Hunter syndrome

We report on the unexpected finding that click modification of iduronyl azides results in a conformational flip of the pyranose ring, which led to the development of a new strategy for the design of superior enzyme substrates for the diagnostic assaying of iduronate-2-sulfatase (I2S), a lysosomal enzyme related to Hunter syndrome. Synthetic substrates are essential in testing newborns for metabolic disorders to enable early initiation of therapy. Our click-flipped iduronyl triazole showed a remarkably better performance with I2S than commonly used O-iduronates. We found that both O- and triazole-linked substrates are accepted by the enzyme, irrespective of their different conformations, but only the O-linked product inhibits the activity of I2S. Thus, in the long reaction times required for clinical assays, the triazole substrate substantially outperforms the O-iduronate. Applying our click-flipped substrate to assay I2S in dried blood spots sampled from affected patients and random newborns significantly increased the confidence in discriminating between these groups, clearly indicating the potential of the click-flip strategy to control the biomolecular function of carbohydrates.

Click-triggered flip of the conformation of a sulfated iduronyl azide afforded a superior enzyme substrate to screen for Hunter syndrome.     

KoBra: A rate constant method for prediction of the diffusion of sorbates inside nanoporous materials at different loadings

We present a new method for calculating the diffusion tensor for the systems of sorbates inside nanoporous materials at different loadings by just using transition rate constants. In addition, a user-friendly program with graphical user interface has been developed and is freely provided to be used ( https://sourceforge.net/projects/kobra/ ). It needs from the user just to provide the values of the unit cell lengths and angles, the transition rate constants for each sorbate, and any spatial constraint between these sorbates. This program is shown to be about 30 times faster than kinetic Monte Carlo method. Application of the method to the problem of diffusion of aromatics in silicalite-1 at different loadings is presented too. © 2019 Wiley Periodicals, Inc.     

Surfactant-induced forces between carbon nanotubes

Dissipative particle dynamics simulations are employed to study surfactant-mediated forces between a pair of perpendicular carbon nanotubes (CNTs) coated by surfactants which form spherical micelles in bulk solution and on the tubes. Two force regimes are observed: at small tube/tube distances the force is attractive, whereas it is repulsive at larger distances. The attractive regime is dominated by a central micelle binding the tubes, while in the repulsive regime the contact region is depleted. The two regimes are separated by a discontinuous transition. The repulsive regime is critical for stabilizing CNT suspensions. Viewing rebundling as a thermally activated process, a connection between the repulsive force and the rebundling rate is established. We find that a larger hydrophilic surfactant headgroup creates a stronger and longer ranged tube/tube force, which reduces the rebundling rate significantly. The longer range originates directly from the further reaching head corona of the adsorbed surfactant layer. The larger magnitude of the force appears to be related to the axial compression force the adsorbed phase can sustain. This compression force appears to be the most critical factor for suspension design.     

Asymmetric potentials and motor effect: a homogenization approach

We provide a mathematical analysis for the appearance of motor effects, i.e., the concentration (as Dirac masses) at one side of the domain, for the solution of a Fokker–Planck system with two components, one with an asymmetric potential and diffusion and one with pure diffusion. The system has been proposed as a model for motor proteins moving along molecular filaments. Its components describe the densities of different conformations of proteins.     

Square wave anodic stripping voltammetry determination of eco-toxic metals in samples of biological and environmental importance

Square wave anodic stripping voltammetry was used in simultaneous determinations of eco-toxic metals (Pb, Cd, Cu and Zn) on bismuth film electrodes. The electrodes were prepared in situ on a glassy-carbon electrode (GCE) from 0.1 M acetate buffer (pH 4.5) containing 200 μg L^?1 of bismuth (III), as well ex situ on electrochemically oxidized graphitized polyacrylonitrile carbon fibres from 200 mg L^?1 Bi(NO₃)₃ in 1% HNO₃ (aqueous) solution. Preparation of a Bi-modified carbon fibre electrode (CFE) was by cation exchange of Bi⁺³ ions for H⁺ of the acidic surface groups of the electro-oxidized carbon fibres, followed by electrochemical reduction to Bi⁰. For the Bi-GCE the linear range was 20–280 μg L^?1 for zinc, 10–100 μg L^?1 for lead, 10–80 μg L^?1 for copper, and 5–50 μg L^?1 for cadmium. For the Bi-CFE it was 20–160 μg L^?1 for zinc, 10–100 μg L^?1 for lead, 10–100 μg L^?1 for copper, and 2–120 μg L^?1 for cadmium. For both kinds of bismuth modified carbon electrodes, low limits of detection and satisfactory precision were achieved. The method was successfully applied to certified reference materials of biological (bovine liver) and environmental (mussel tissue) importance.