Dinuclear Zn(II) catalysts as biomimics of RNA and DNA phosphoryl transfer enzymes: changing the medium from water to alcohol provides enzyme‐like rate enhancements

Phosphodiesters are notoriously hydrolytically inert compounds that are demonstrated to have large accelerations of P‐OR cleavage promoted by transition and lanthanide metal ions in methanol and ethanol media. This review commentary describes recent findings of how a simple mononuclear and a dinuclear Zn(II) complex promote the cleavage of a series of RNA models and DNA models in alcohol media. The discussion centers on the analysis of the mechanisms of cleavage, energetics of the catalytic process, on recent findings of electrophilic assistance of leaving group departure, and the observation of a rapid hydrolytic reaction of a DNA model promoted by the dinuclear Zn(II) complex in ethanol containing less than 2% water. Copyright © 2009 John Wiley & Sons, Ltd.     

Effect of substituent groups of porphyrins on the electroluminescent properties of porphyrin‐doped OLED devices

Six tetraphenylporphyrins (TRPPH₂) with different horizontal substituents R (R = H, CH₃, OH, F, Cl, Br) were synthesized, and the organic light‐emitting diode (OLED) devices with a general configuration of ITO/TPD/Alq₃:2%TRPPH₂/Alq₃/Al were prepared. The substituted TRPPH₂ was used as the host dopant, 4,4‐bis‐(m‐tolyphenylamino)biphenyl (TPD) was used as a hole‐transporting material, and aluminum tris(8‐quinolinolato) (Alq₃) was used as an electron‐transporting material. The electroluminescent (EL) properties of these devices were studied to understand the light emitting properties of the substituted TRPPH₂. Previous studies have found that the color emitted by the devices was dependent on the TRPPH₂ dye concentration. The electronic effect of the horizontal substituents R of TRPPH₂ influenced the turn‐on voltage, brightness, and power efficiency of the devices. Also, the electroluminescence performance of the porphyrin‐doped OLED devices depended on the effectual overlaps between the emission of electron‐transporting material and the absorption of the dopants. This means that it is possible to evaluate the electroluminescence performance of the porphyrin‐doped OLED devices based on the emission of electron‐transporting material and the absorption of the dopants. Copyright © 2009 John Wiley & Sons, Ltd.     

Intramolecular Diels–Alder reaction in enyne–allenes: a computational investigation and comparison with the Myers–Saito and Schmittel reactions

The reaction mechanisms as well as substituted effect and solvent effect of the enyne–allenes are investigated by Density Functional Theory (DFT) method and compared with the Myers–Saito and Schmittel reactions. The Myers–Saito reaction of non‐substituted enyne–allenes is kinetically and thermodynamically favored as compared to the Schmittel reaction; while the concerted [4 + 2] cycloaddition is only 1.32 kcal/mol higher than the C₂? C₇ cyclization and more exothermic (Δ_RE = ?69.38 kcal/mol). For R₁ = CH₃ and t‐Bu, the increasing barrier of the C₂? C₇ cyclization is higher than that for the C₂? C₆ cyclization because of the steric effect, so the increased barrier of the [4 + 2] cycloaddition is affected by such substituted electron‐releasing group. Moreover, the strong steric effect of R₁ = t‐Bu would shift the C₂? C₇ cyclization to the [4 + 2] cycloaddition. On the other hand, for R₁ = Ph, NH₂, O^?, NO₂, and CN substituents, the barrier of the C₂? C₆ cyclization would be more diminished than the C₂? C₇ cyclization due to strong mesomeric effect; the reaction path of C₂? C₇ cyclization would also shift to the [4 + 2] cycloaddition. The solvation does not lead to significant changes in the potential‐energy surface of the reaction except for the more polar surrounding solvent such as dimethyl sulfoxide (DMSO), or water. Copyright © 2009 John Wiley & Sons, Ltd.     

Fe valence state at the surface of the Fe0.5Cu0.5Cr2S4 spinel

Here we present X‐ray absorption measurements of a vacuum cleaved Fe_0.5Cu_0.5Cr₂S₄ single crystal. Measurements at different positions on the cleaved sample surface clearly reveal a difference between the valence state of the Fe ions in the sur‐ face layers and the valency of the Fe ions present in the bulk. These results confirm the findings of recent measurements outlined previously. (© 2010 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Accurate standard‐based quantification of X‐ray fluorescence data using metal‐contaminated plant tissue

Quantitative X‐ray fluorescence (XRF) measurements have been conducted on naturally lead‐contaminated samples. The calibration procedure using the ratio of fluorescence to Compton scattered radiation was investigated using Monte Carlo simulation. Experimental results with low‐energy photons (14 keV) and simulations show a very good linearity of the fluorescence to Compton ratio as a function of metal concentration. Lead (Pb), iron (Fe) and zinc (Zn) are measured in samples of Phaseolus vulgaris (bean seeds) that have been grown using a nutritive solution with different Pb dopings. Naturally contaminated samples are thus obtained. The calibration must be done for fixed conditions of X‐ray energy and scattering angle, while X‐ray beam intensity and detector to sample distance can change from one sample to another. Simulation allows to evaluate the matrix effect on the calibration curve, and shows that linearity is preserved even in the presence of other heavy elements in the fluorescence spectrum. However, calibration must be done using samples with similar matrix as it affects the slope of the curve. Copyright © 2010 John Wiley & Sons, Ltd.     

Assessment of high-resolution methods for numerical simulations of compressible turbulence with shock waves

Flows in which shock waves and turbulence are present and interact dynamically occur in a wide range of applications, including inertial confinement fusion, supernovae explosion, and scramjet propulsion. Accurate simulations of such problems are challenging because of the contradictory requirements of numerical methods used to simulate turbulence, which must minimize any numerical dissipation that would otherwise overwhelm the small scales, and shock-capturing schemes, which introduce numerical dissipation to stabilize the solution. The objective of the present work is to evaluate the performance of several numerical methods capable of simultaneously handling turbulence and shock waves. A comprehensive range of high-resolution methods (WENO, hybrid WENO/central difference, artificial diffusivity, adaptive characteristic-based filter, and shock fitting) and suite of test cases (Taylor–Green vortex, Shu–Osher problem, shock-vorticity/entropy wave interaction, Noh problem, compressible isotropic turbulence) relevant to problems with shocks and turbulence are considered. The results indicate that the WENO methods provide sharp shock profiles, but overwhelm the physical dissipation. The hybrid method is minimally dissipative and leads to sharp shocks and well-resolved broadband turbulence, but relies on an appropriate shock sensor. Artificial diffusivity methods in which the artificial bulk viscosity is based on the magnitude of the strain-rate tensor resolve vortical structures well but damp dilatational modes in compressible turbulence; dilatation-based artificial bulk viscosity methods significantly improve this behavior. For well-defined shocks, the shock fitting approach yields good results.     

The early high-energy afterglow emission from short GRBs

We calculate the high energy afterglow emission from short Gamma-Ray Bursts (SGRBs) in the external shock model. There are two possible components contributing to the high energy afterglow: electron synchrotron emission and synchrotron self-Compton (SSC) emission. We find that for typical parameter values of SGRBs, the early high-energy afterglow emission in 10 MeV-10 GeV is dominated by synchrotron emission. For a burst occurring at redshift z = 0.1, the high-energy emission can be detectable by Fermi LAT if the blast wave has energy E ⩾ 10⁵¹ ergs and the fraction of electron energy ɛ _e ⩾ 0.1. This provides a possible explanation for the high energy tail of SGRB 081024B.

     

Seed‐mediated growth method for electroless deposition of AgNPs on glass substrates for use in SERS measurements

In this work, an electroless deposition method for silver nanoparticles (AgNPs) on glass substrates was developed for use in surface‐enhanced Raman scattering (SERS) measurements. To obtain evenly distributed AgNPs of suitable size on the glass substrates, a seeding procedure was utilized as a pretreatment before the electroless deposition of AgNPs. The AgNPs thus formed were affected by both the seeding and growing procedures. To optimize the procedures for preparation of SERS substrates, several factors, including reaction time, the concentration of silver ions, and the concentration of reducing agents (glucose) for seeding and growing procedures, were varied. The morphologies of the seeds and the resulting AgNPs on the glass substrates were characterized by field‐emission scanning electron microscopy (FE‐SEM) and correlated with the SERS signals from probing with para‐nitrothiophenol (pNTP). The results indicated that only the seeding time and the concentration of silver ions significantly influenced the distribution and sizes of the Ag seeds on the substrates. In the growing procedures, both the concentration of silver nitrate and the reducing agent affected the morphologies of the resulting AgNPs and, hence, the SERS signals. The substrates prepared using this newly developed method offer 2–5 times improvement of the SERS signals compared to substrates prepared without seed treatment. Also, the AgNPs prepared by this method can be easily controlled to designated sizes with even spatial and size distributions. Copyright © 2009 John Wiley & Sons, Ltd.     

Raman and surface‐enhanced Raman spectroscopic studies of the 15‐mer DNA thrombin‐binding aptamer

Aptamers are single‐stranded oligonucleotides that selectively bind to their target molecules owing to their ability to form secondary structures and shapes. The 15‐mer (5′‐GGTTGGTGTGGTTGG‐3′) DNA thrombin‐binding aptamer (TBA) binds to thrombin following the formation of a quadruplex structure via the Hoogsten‐type G–G interactions. In the present study, Raman and SERS spectra of TBA and thiolated TBA (used to facilitate covalent bonding to metal nanoparticle) in different conditions are investigated. The spectra of the two analogs exhibit vibrations, such as the C8N7 H2 deformation band at ∼1480 cm⁻¹ of the guanine tetrad, that are characteristic of the quadruplex structure in the presence of K⁺ ions or at low temperature. Interestingly, SERS spectra of the two analogs differ markedly from their respective normal Raman spectra, possibly due to changes in the conformation of the aptamer upon binding, as well as to the specific interaction of individual vibrational modes with the metal surface. In addition, the SERS spectra of the thiolated aptamer show significant changes with different concentrations, which may be due to different orientation of the molecule with respect to the metal surface. This study provides useful information for the development of label‐free aptamer‐based SERS sensors and assays. Copyright © 2009 John Wiley & Sons, Ltd.     

Raman and SERS study of metoclopramide at different pH values

Conjugate acid–base forms of the drug metoclopramide were investigated by Raman spectroscopy in aqueous solutions and by surface‐enhanced Raman scattering (SERS), when the molecules were adsorbed on colloidal silver surfaces. Raman spectra were recorded at pH values below 8, metoclopramide being poorly water soluble at higher pH values. The SERS spectra of metoclopramide were recorded in the 3–11 pH range, even in spite of its low solubility at basic pH values. The Raman and SERS spectra were assigned by means of density functional theory (DFT) calculations. By monitoring several SERS marker bands, the protonated, neutral or the coexistence of both molecular species adsorbed on the colloidal silver particles could be evidenced. The adsorbate orientation was deduced to be perpendicular to the metal surface for the protonated molecular species and tilted for the neutral metoclopramide molecular species. Copyright © 2009 John Wiley & Sons, Ltd.