Net charge changes in the calculation of relative ligand‐binding free energies via classical atomistic molecular dynamics simulation

The calculation of binding free energies of charged species to a target molecule is a frequently encountered problem in molecular dynamics studies of (bio‐)chemical thermodynamics. Many important endogenous receptor‐binding molecules, enzyme substrates, or drug molecules have a nonzero net charge. Absolute binding free energies, as well as binding free energies relative to another molecule with a different net charge will be affected by artifacts due to the used effective electrostatic interaction function and associated parameters (e.g., size of the computational box). In the present study, charging contributions to binding free energies of small oligoatomic ions to a series of model host cavities functionalized with different chemical groups are calculated with classical atomistic molecular dynamics simulation. Electrostatic interactions are treated using a lattice‐summation scheme or a cutoff‐truncation scheme with Barker–Watts reaction‐field correction, and the simulations are conducted in boxes of different edge lengths. It is illustrated that the charging free energies of the guest molecules in water and in the host strongly depend on the applied methodology and that neglect of correction terms for the artifacts introduced by the finite size of the simulated system and the use of an effective electrostatic interaction function considerably impairs the thermodynamic interpretation of guest‐host interactions. Application of correction terms for the various artifacts yields consistent results for the charging contribution to binding free energies and is thus a prerequisite for the valid interpretation or prediction of experimental data via molecular dynamics simulation. Analysis and correction of electrostatic artifacts according to the scheme proposed in the present study should therefore be considered an integral part of careful free‐energy calculation studies if changes in the net charge are involved. © 2013 The Authors Journal of Computational Chemistry Published by Wiley Periodicals, Inc.     

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.     

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.     

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.     

Metabolism of JWH-015, JWH-098, JWH-251, and JWH-307 in silico and in vitro: a pilot study for the detection of unknown synthetic cannabinoids metabolites

This pilot study was performed to study the main metabolic reactions of four synthetic cannabinoids: JWH-015, JWH-098, JWH-251, and JWH-307 in order to setup a screening method for the detection of main metabolites in biological fluids. In silico prediction of main metabolic reactions was performed using MetaSite^? software. To evaluate the agreement between software prediction and experimental reactions, we performed in vitro experiments on the same JWHs using rat liver slices. The obtained samples were analyzed by liquid chromatography-quadrupole time-of-flight and the identification of metabolites was executed using Mass-MetaSite^? software that automatically assigned the metabolite structures to the peaks detected based on their accurate masses and fragmentation. A comparison between the experimental findings and the in silico metabolism prediction using MetaSite^? software showed a good accordance between experimental and in silico data. Thus, the use of in silico metabolism prediction might represent a useful tool for the forensic and clinical toxicologist to identify possible main biomarkers for synthetic cannabinoids in biological fluids, especially urine, following their administration.

QuEChERS sample preparation for the determination of pesticides and other organic residues in environmental matrices: a critical review

Quick, Easy, Cheap, Effective, Rugged, and Safe (QuEChERS) is an extraction and clean-up technique originally developed for recovering pesticide residues from fruits and vegetables. Since its introduction, and until December 2013, about 700 papers have been published using the QuEChERS technique, according to a literature overview carried out using SciFinder, Elsevier SciVerse, and Google search engines. Most of these papers were dedicated to pesticide multiresidue analysis in food matrices, and this topic has been thoroughly reviewed over recent years. The QuEChERS approach is now rapidly developing beyond its original field of application to analytes other than pesticides, and matrices other than food, such as biological fluids and non-edible plants, including Chinese medicinal plants. Recently, the QuEChERS concept has spread to environmental applications by analyzing not only pesticides but also other compounds of environmental concern in soil, sediments, and water. To the best of our knowledge, QuEChERS environmental applications have not been reviewed so far; therefore, in this contribution, after a general discussion on the evolution and changes of the original QuEChERS method, a critical survey of the literature regarding environmental applications of conventional and modified QuEChERS methodology is provided. The overall recoveries obtained with QuEChERS and other extraction approaches (e.g., accelerated solvent extraction, ultrasonic solvent extraction, liquid/solid extraction, and soxhlet extraction) were compared, providing evidence for QuEChERS higher recoveries for various classes of compounds, such as biopesticides, chloroalkanes, phenols, and perfluoroalkyl substances. The role of physicochemical properties of soil (i.e., clay and organic carbon content, as well as cation exchange capacity) and target analytes (i.e., log K_OW, water solubility, and vapor pressure) were also evaluated in order to interpret recovery and matrix effect data.