Two Intercalation Mechanisms of Oxazole Yellow Dimer (YOYO-1) into DNA

The oxazole yellow dye, YOYO-1 (a symmetric homodimer), is a commonly used molecule for staining DNA. We applied the brightness analysis to study the intercalation of YOYO-1 into the DNA. We distinguished two binding modes of the dye to dsDNA: mono-intercalation and bis-intercalation. Bis-intercalation consists of two consecutive mono-intercalation steps, characterised by two distinct equilibrium constants (with the average number of base pair per binding site equals 3.5): K1=3.36±0.43×107M−1 and K2=1.90±0.61×105M−1, respectively. Mono-intercalation dominates at high concentrations of YOYO-1. Bis-intercalation occurs at low concentrations.     

Common Shortcomings in Study on Radiopharmaceutical Design Research: A Case Study of 99mTc-Labelled Methotrexate

The aim of the work carried out was to draw attention to shortcomings that often appear at the stage of designing new radiopharmaceuticals. Based on a case study of ^99mTc-labelled methotrexate, this article describes frequent mistakes or misconceptions present not only in the referenced studies, but also in numerous radiopharmaceutical studies. The recommendations provided in this article highlight fundamental aspects of the credibility of radiopharmaceutical scientific research leading to the reliable results.     

Anharmonicity and Spectra–Structure Correlations in MIR and NIR Spectra of Crystalline Menadione (Vitamin K3)

Mid-infrared (MIR) and near-infrared (NIR) spectra of crystalline menadione (vitamin K₃) were measured and analyzed with aid of quantum chemical calculations. The calculations were carried out using the harmonic approach for the periodic model of crystal lattice and the anharmonic DVPT2 calculations applied for the single molecule model. The theoretical spectra accurately reconstructed the experimental ones permitting for reliable assignment of the MIR and NIR bands. For the first time, a detailed analysis of the NIR spectrum of a molecular system based on a naphthoquinone moiety was performed to elucidate the relationship between the chemical structure of menadione and the origin of the overtones and combination bands. In addition, the importance of these bands during interpretation of the MIR spectrum was demonstrated. The overtones and combination bands contribute to 46.4% of the total intensity of menadione in the range of 3600–2600 cm⁻¹. Evidently, these bands play a key role in shaping of the C-H stretching region of MIR spectrum. We have shown also that the spectral regions without fundamentals may provide valuable structural information. For example, the theoretical calculations reliably reconstructed numerous overtones and combination bands in the 4000–3600 and 2800–1800 cm⁻¹ ranges. These results, provide a comprehensive origin of the fundamentals, overtones and combination bands in the NIR and MIR spectra of menadione, and the relationship of these spectral features with the molecular structure.     

Methodological studies of the determination of 99Tc in matrix-rich environmental samples

A few experiments testing technetium behavior at different conditions for complex matrixes (soils, sediments) were performed. It was confirmed that the incineration of samples soaked with ammonia can be done without technetium losses. Next, for the precipitation of iron(III) hydroxide at different pH levels, the degree of co-precipitation of technetium was studied. It can be helpful during purification of very matrix-rich and massive samples. Finally the technetium and rhenium fractionation during separation of technetium from the environmental samples was studied. This test clearly showed limitations for using Re as yield tracer during ⁹⁹Tc analyses in case of mineral matrixes.     

Solid phase microextraction fills the gap in tissue sampling protocols

Metabolomics and biomarkers discovery are an integral part of bioanalysis. However, untargeted tissue analysis remains as the bottleneck of such studies due to the invasiveness of sample collection, as well as the laborious and time-consuming sample preparation protocols. In the current study, technology integrating in vivo sampling, sample preparation and global extraction of metabolites – solid phase microextraction was presented and evaluated during liver and lung transplantation in pig model. Sampling approaches, including selection of the probe, transportation, storage conditions and analyte coverage were discussed. The applicability of the method for metabolomics studies was demonstrated during lung transplantation experiments.     

Electrochemical Characteristics of Discrete,Uniform, and Monodispersed Hollow Mesoporous Carbon Spheres in Double‐Layered Supercapacitors

Core–shell‐structured mesoporous silica spheres were prepared by using n‐octadecyltrimethoxysilane (C18TMS) as the surfactant. Hollow mesoporous carbon spheres with controllable diameters were fabricated from core–shell‐structured mesoporous silica sphere templates by chemical vapor deposition (CVD). By controlling the thickness of the silica shell, hollow carbon spheres (HCSs) with different diameters can be obtained. The use of ethylene as the carbon precursor in the CVD process produces the materials in a single step without the need to remove the surfactant. The mechanism of formation and the role played by the surfactant, C18TMS, are investigated. The materials have large potential in double‐layer supercapacitors, and their electrochemical properties were determined. HCSs with thicker mesoporous shells possess a larger surface area, which in turn increases their electrochemical capacitance. The samples prepared at a lower temperature also exhibit increased capacitance as a result of the Brunauer–Emmett–Teller (BET) area and larger pore size.     

Gas chromatography with mass spectrometric,atomic emission and Fourier transform infrared spectroscopic detection as complementary analytical techniques for the identification of unknown impurities in pharmaceutical analysis

An example of the complementary use of GC-MS. GC-AED and GC-FT-IR is described for efficient structure elucidation of an unknown impurity in pharmaceutical analysis. None of the analytical techniques could solve the structure of the unknown impurity alone; identification was, however, straightforward by combining the available spectroscopic information. GC-MS provided information about structural fragments and molecular mass of the unknown compound. GC-AED was used for confirmation of the occurrence of the individual elements in the structure and to enable calculation of the empirical formula. GC-FT-IR gave valuable information regarding functional groups in the molecule.     

Cucurbit[6]uril pseudorotaxanes: distinctive gas-phase dissociation and reactivity

Cucurbit[6]uril forms a doubly charged complex with 1,4-butanediammonium cation that is observed using electrospray ionization Fourier transform mass spectrometry. Such 1:1 complexes are not observed for the smaller cucurbit[5]uril, which forms a 2:1 ammonium:cucurbituril complex instead. The 1:1 complex with cucurbit[6]uril is difficult to fragment via collisional activation; when it does fragment, both breakup of the cucurbituril cage and loss of the amine are observed. Further, the complex reacts with tert-butylamine via slow adduction. In contrast, nonrotaxane analogues (such as doubly charged 2:1 complexes of either protonated 1,4-butanediamine or protonated ethylenediamine with cucurbit[6]uril) fragment via easy loss of the intact amine upon collisional activation and react with tert-butylamine via rapid displacement of the original amine. On the basis of stoichiometry, fragmentation behavior, and reactivity, we conclude that the doubly charged complex of cucurbit[6]uril with 1,4-butanediammonium is a gas-phase pseudorotaxane.     

Morphology and molecular organisation of liquid-crystalline perylene-3,4,9,10-tetra-(n-hexylester) deposited on a solid substrate

Liquid-crystalline perylene-3,4,9,10-tetra-(n-hexylester) forms characteristic dendritic or flower-like structures at room temperature when it is deposited on a hydrophilic glass substrate using the zone-casting technique. It was found that such unique structures were not possible to be created simply by recrystallisation of this dye from a liquid-crystalline columnar phase. On the basis of the observations using a confocal microscope and the study of wide angle X-ray scattering (WAXS) as well as the analysis of the absorption and fluorescence spectra, some conclusions, concerning the molecular organisation in the dendritic structure, are drawn. Based on the research, one can assume that the dendrites are formed by columnar molecular aggregates with the column axes parallel to the substrate. Such an organisation of the molecules can be interesting from the point of view of organic electronics.     

An efficient parallel algorithm for the calculation of unrestricted canonical MP2 energies

We present details of our efficient implementation of full accuracy unrestricted open‐shell second‐order canonical Møller–Plesset (MP2) energies, both serial and parallel. The algorithm is based on our previous restricted closed‐shell MP2 code using the Saebo–Almlöf direct integral transformation. Depending on system details, UMP2 energies take from less than 1.5 to about 3.0 times as long as a closed‐shell RMP2 energy on a similar system using the same algorithm. Several examples are given including timings for some large stable radicals with 90+ atoms and over 3600 basis functions. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011