Molecular dynamics simulation of configurational ensembles compatible with experimental FRET efficiency data through a restraint on instantaneous FRET efficiencies

Förster resonance energy transfer (FRET) measurements are widely used to investigate (bio)molecular interactions or/and association. FRET efficiencies, the primary data obtained from this method, give, in combination with the common assumption of isotropic chromophore orientation, detailed insight into the lengthscale of molecular phenomena. This study illustrates the application of a FRET efficiency restraint during classical atomistic molecular dynamics simulations of a mutant mastoparan X peptide in either water or 7 M aqueous urea. The restraint forces acting on the donor and acceptor chromophores ensure that the sampled peptide configurational ensemble satisfies the experimental primary data by modifying interchromophore separation and chromophore transition dipole moment orientations. By means of a conformational cluster analysis, it is seen that indeed different configurational ensembles may be sampled without and with application of the restraint. In particular, while the FRET efficiency and interchromophore distances monitored in an unrestrained simulation may differ from the experimentally‐determined values, they can be brought in agreement with experimental data through usage of the FRET efficiency restraining potential. Furthermore, the present results suggest that the assumption of isotropic chromophore orientation is not always justified. The FRET efficiency restraint allows the generation of configurational ensembles that may not be accessible with unrestrained simulations, and thereby supports a meaningful interpretation of experimental FRET results in terms of the underlying molecular degrees of freedom. Thus, it offers an additional tool to connect the realms of computer and wet‐lab experimentation. © 2014 Wiley Periodicals, Inc.     

Implementation of the k 0-standardization method for analysis of geological samples at the Neutron Activation Analysis Laboratory, São Paulo, Brazil

The Neutron Activation Analysis Laboratory (LAN-IPEN) has been analysing geological samples for many years with the INAA comparative method, for geochemical and environmental research. This study presents the results obtained in the implementation of the k ₀-standardization method at LAN-IPEN, for geological samples analysis, by using the program k ₀-IAEA, provided by the International Atomic Energy Agency (IAEA). The thermal to epithermal flux ratio f and the shape factor α of the epithermal flux distribution of the IEA-R1 nuclear reactor of IPEN were determined for the pneumatic irradiation facility and one selected irradiation position, for short and long irradiations, respectively. To obtain these factors, the “bare triple-monitor” method with ¹⁹⁷Au–⁹⁶Zr–⁹⁴Zr was used. In order to validate the methodology, the geological reference materials basalts JB-1 (GSJ) and BE-N (IWG-GIT), andesite AGV-1 (USGS), granite GS-N (ANRT), SOIL-7 (IAEA) and sediment Buffalo River Sediment (NIST–BRS-8704), which represent different geological matrices, were analysed. The concentration results obtained agreed with assigned, with bias <10 % except for Zn in AGV-1. The U-score test showed that all results, except Mg in JB-1, are within 95 % confidence interval. These results indicate excellent possibilities of using this parametric method at the LAN-IPEN for geochemical and environmental studies.     

Multivariate optimization of a headspace solid‐phase microextraction method followed by gas chromatography with mass spectrometry for the determination of terpenes in Nicotiana langsdorffii

A simple and sensitive procedure based on headspace solid‐phase microextraction and gas chromatography with mass spectrometry was developed for the determination of five terpenes (α‐pinene, limonene, linalool, α‐terpineol, and geraniol) in the leaves of Nicotiana langsdorffii. The microextraction conditions (extraction temperature, equilibration time, and extraction time) were optimized by means of a Doehlert design. The experimental design showed that, for α‐pinene and limonene, a low temperature and a long extraction time were needed for optimal extraction, while linalool, α‐terpineol, and geraniol required a high temperature and a long extraction time. The chosen compromise conditions were temperature 60°C, equilibration time 15 min and extraction time 50 min. The main analytical figures of the optimized method were evaluated; LODs ranged from 0.07 ng/g (α‐pinene) to 8.0 ng/g (geraniol), while intraday and interday repeatability were in the range 10–17% and 9–13%, respectively. Finally, the procedure was applied to in vitro wild‐type and transgenic specimens of N. langsdorffii subjected to abiotic stresses (chemical and heat stress). With the exception of geraniol (75–374 ng/g), low concentration levels of terpenes were measured (ng/g level or lower); some interesting variations in terpene concentration induced by abiotic stress were observed.     

Multiresidue analysis of quinolones in water by ultra‐high perfomance liquid chromatography with tandem mass spectrometry using a simple and effective sample treatment

A rapid and simple analytical method has been developed for the determination of 19 quinolones in environmental water samples using ultra high performance liquid chromatography with tandem mass spectrometry. Chromatographic and detection conditions have been optimized and the separation was achieved in less than 4 min. The separation was carried out using a new‐generation column filled with superficially porous particles, resulting in lower backpressure and better resolution than totally porous particle columns. The quinolones were detected by electrospray ionization in positive mode using multiple‐reaction monitoring mode for acquisition. A sample treatment based on liquid–liquid extraction and phase separation via salting‐out was employed to achieve a fast and simple extraction that enables the multiresidue analysis. The method has been validated for an environmental well water sample from a mountain area. Very low limits of detection (between 10 and 90 ng/L) with relative standard deviations lower than 16.5% and recoveries higher than 73% were achieved. Moreover, well waters from different origins (mountain and coast areas and irrigated land) have been evaluated and similar results were obtained.     

Study of the retention behavior of iodinated X‐ray contrast agents in hydrophilic interaction liquid chromatography,comparing bare silica and zwitterionic stationary phases

Iodinated X‐ray contrast media are the most widely used pharmaceuticals for intravascular administration in X‐ray diagnostic procedures. The increasing concern of the fate of these compounds into the environment has led to the development of analytical methods to determine them. However, these methods present problems due to the polar character of these analytes. In this paper, hydrophilic interaction LC is presented as an alternative technique. The retention of iodinated X‐ray contrast media was studied in two bare silica phases with different particle designs (i.e. porous and Fused Core?) and a zwitterionic sulfoalkylbetaine phase. The effect of the most important parameters of the mobile phase was studied for each stationary phase. It was observed that optimal mobile phase conditions included buffers with a high buffering capacity. Additionally, the retention mechanisms involved were studied in order to provide some insight into the possible occurring interactions. The contributions of partition and adsorption and the effect of the temperature on the retention of analytes were evaluated on all of the stationary phases.     

Physicochemical and adsorption properties of hypercross‐linked polystyrene with ultimate cross‐linking density

The paper describes unexpected properties of hypercross‐linked polystyrenes with ultimate cross‐linking degrees of 300, 400, and 500%, where three, four, or five methylene links, respectively, could bind each polystyrene phenyl ring to its spacious neighbors. The polymers exhibit a strong electron spin resonance signal, unusual spectra in IR, UV, and visible ranges, and they are not typical dielectrics. The nonfunctionalized hypercross‐linked polymers absorb significant amounts of inorganic acids, salts, and bases due to interactions of protons or other cations with electron‐donating fragments of the aromatic network with the high extent of mutual connectivity and also due to dispersion interactions of anions with the polymer matrix.     

Determination of sulfonamides in milk samples by HPLC with amperometric detection using a glassy carbon electrode modified with multiwalled carbon nanotubes

A sensitive and accurate method for determining five sulfonamides based on HPLC with amperometric detection and using a glassy carbon electrode modified with multiwalled carbon nanotubes is proposed. Optimal conditions for the quantitative separation of selected sulfonamides were studied, and glassy carbon electrodes with and without modification with carbon nanotubes were systematically investigated as electrodic materials. Statistical analysis of the obtained results demonstrated that these modified electrodes achieved considerably better stability and sensitivity than the conventional unmodified ones. Detection limits were in the 1.2–6.0 ng/mL range. The usefulness of the method was demonstrated by the analysis of milk samples, taking into account the European legislation on residues in food products, following both a screening method to classify the samples and a confirmation method to provide more detailed information in the case of positive samples.     

Application of liquid chromatography quadrupole time-of-flight mass spectrometry to the identification of acetamiprid transformation products generated under oxidative processes in different water matrices

This work allowed the identification of major transformation products (TPs) of acetamiprid (ACTM) during Fenton process. Acetamiprid is a chloronicotinoid insecticide widely used around the world for its characteristics (high insecticidal activity, good systemic properties, suitable field stability, etc.). The degradation of the parent molecule and the identification of the main TPs were evaluated in different water matrices (demineralized water and real agro-food industrial wastewater). TPs of acetamiprid generated by Fenton experiments were monitored and identified by liquid chromatography quadrupole time-of-flight tandem mass spectrometry (LC–QTOF–MS/MS). Up to 14 TPs were characterized based on the accurate mass of the molecular ion and fragment ions obtained in both full-scan and MS/MS modes. Most of them were eliminated after 75 min of treatment time in demineralized water. However, in real agro-food industrial wastewater, most of them were eliminated at 90 min of treatment time, demonstrating the influence of the matrix composition on the studied compound degradation.