Numerical approximation of AR‐XPS spectra for rough surfaces considering the effect of electron shadowing

A computational scheme is presented that takes into account the topography, i.e. the shadowing and hence the local emission angle of the electrons when evaluating AR‐XPS data of macroscopic rough surfaces. The topography of the sample surface is supposed to be recorded by atomic force microscopy and/or optical microscopy. The emitted photoelectrons are simulated based on an extension of the Beer–Lambert law that includes the shadowing, the current local emission angle, and the geometrical instrument setup. The obtained angle‐resolved XPS spectra are optimized in accordance with experimental ones via a self‐consistent minimization algorithm that also allows one to determine the layer thicknesses of the corrugated sample. In order to validate the proposed numerical scheme, the simulation program simulation of electron spectra for surface analysis is used. An additional analysis is then performed considering only experimental data. The numerical scheme gives good agreement in simulation–simulation as well as simulation–experiment comparisons and permits a comprehensible interpretation of the measured data. Copyright © 2014 John Wiley & Sons, Ltd.     

Effect of magnesium and titanium on the cathodic behaviour of aluminium in nitric acid

Cathodic polarization of aluminium and Al–0.18 wt.% Mg and Al–0.08 wt.% Ti alloys in 0.24 mol dm^?3 nitric acid solution at 38 °C has been employed to assist understanding of the roles of alloying elements in electrograining. The findings indicate that additions of magnesium and titanium to aluminium accelerate the corrosion of the substrate under the alkalization caused by the cathodic reactions. The accelerated dissolution and the consequent formation of hydrated alumina result in a decreased net cathodic current density in potentiostatic and potentiodynamic polarization conditions relative to the behaviour of aluminium. Copyright © 2014 John Wiley & Sons, Ltd.     

Electrodeposition and characterization of Zn–Sn alloy coatings from a deep eutectic solvent based on choline chloride for corrosion protection

With the aim of obtaining high corrosion resistant Zn–Sn alloy coatings from an ionic liquid, the effects of electrodeposition potential and electrolyte composition on the electrodeposition behavior, film composition, morphology and corrosion performance were investigated. Cyclic voltammograms indicate that Zn and Sn were co‐deposited at distinct reduction potentials as pure Zn and Sn elements. In addition, the phase composition analysis also showed that the obtained Zn–Sn alloy deposits (8 wt.%–45 wt.% Zn) consist of a two‐phase mechanical mixture of small aggregates of Zn and Sn metals. The Zn content of the alloy significantly increases as the electrodeposition potential and electrolyte Zn (II)/Sn (II) ratio increase. The corrosion performance study of the obtained Zn–Sn coatings showed that they have a passivation behavior and their corrosion resistance increases as the alloy‐Sn content increases. To improve their morphological properties, ethylene diamine tetraacetic acid additive was introduced into the electrolyte and greatly improved the morphology and corrosion resistance of the deposits. For the first time, it was shown that high corrosion resistance Zn–Sn coatings can be obtained from ionic liquids. Copyright © 2014 John Wiley & Sons, Ltd.     

Nucleic acid reactivity: Challenges for next‐generation semiempirical quantum models

Semiempirical quantum models are routinely used to study mechanisms of RNA catalysis and phosphoryl transfer reactions using combined quantum mechanical (QM)/molecular mechanical methods. Herein, we provide a broad assessment of the performance of existing semiempirical quantum models to describe nucleic acid structure and reactivity to quantify their limitations and guide the development of next‐generation quantum models with improved accuracy. Neglect of diatomic differential overlap and self‐consistent density‐functional tight‐binding semiempirical models are evaluated against high‐level QM benchmark calculations for seven biologically important datasets. The datasets include: proton affinities, polarizabilities, nucleobase dimer interactions, dimethyl phosphate anion, nucleoside sugar and glycosidic torsion conformations, and RNA phosphoryl transfer model reactions. As an additional baseline, comparisons are made with several commonly used density‐functional models, including M062X and B3LYP (in some cases with dispersion corrections). The results show that, among the semiempirical models examined, the AM1/d‐PhoT model is the most robust at predicting proton affinities. AM1/d‐PhoT and DFTB3‐3ob/OPhyd reproduce the MP2 potential energy surfaces of 6 associative RNA phosphoryl transfer model reactions reasonably well. Further, a recently developed linear‐scaling “modified divide‐and‐conquer” model exhibits the most accurate results for binding energies of both hydrogen bonded and stacked nucleobase dimers. The semiempirical models considered here are shown to underestimate the isotropic polarizabilities of neutral molecules by approximately 30%. The semiempirical models also fail to adequately describe torsion profiles for the dimethyl phosphate anion, the nucleoside sugar ring puckers, and the rotations about the nucleoside glycosidic bond. The modeling of pentavalent phosphorus, particularly with thio substitutions often used experimentally as mechanistic probes, was problematic for all of the models considered. Analysis of the strengths and weakness of the models suggests that the creation of robust next‐generation models should emphasize the improvement of relative conformational energies and barriers, and nonbonded interactions. © 2015 Wiley Periodicals, Inc.     

Dividing a complex reaction involving a hypervalent iodine reagent into three limiting mechanisms by ab initio molecular dynamics

The electrophilic N‐trifluoromethylation of MeCN with a hypervalent iodine reagent to form a nitrilium ion, that is rapidly trapped by an azole nucleophile, is thought to occur via reductive elimination (RE). A recent study showed that, depending on the solvent representation, the S_N2 is favoured to a different extent over the RE. However, there is a discriminative solvent effect present, which calls for a statistical mechanics approach to fully account for the entropic contributions. In this study, we perform metadynamic simulations for two trifluoromethylation reactions (with N‐ and S‐nucleophiles), showing that the RE mechanism is always favoured in MeCN solution. These computations also indicate that a radical mechanism (single electron transfer) may play an important role. The computational protocol based on accelerated molecular dynamics for the exploration of the free energy surface is transferable and will be applied to similar reactions to investigate other electrophiles on the reagent. Based on the activation parameters determined, this approach also gives insight into the mechanistic details of the trifluoromethylation and shows that these commonly known mechanisms mark the limits within which the reaction proceeds. © 2015 Wiley Periodicals, Inc.     

Properties of nucleic acid staining dyes used in gel electrophoresis

Nucleic acid staining dyes are used for detecting nucleic acids in electrophoresis gels. Historically, the most common dye used for gel staining is ethidium bromide, however due to its toxicity and mutagenicity other dyes that are safer to the user and the environment are preferred. This Short Communication details the properties of dyes now available and their sensitivity for detection of DNA and their ability to permeate the cell membrane. It was found that GelRed? was the most sensitive and safest dye to use with UV light excitation, and both GelGreen? and Diamond? Nucleic Acid Dye were sensitive and the safer dyes using blue light excitation.