Conformational investigation of some macrobicyclic compounds and of their monoprotonated cations through a comparison between X-ray crystal structures and molecular dynamics simulations

Abstract

In preceding works, which have dealt with the synthesis and characterisation of a series of macrobicyclic compounds with five donor atoms, the unusually high basicity constants of these polyaminic cage-like molecules have been ascribed to the inclusion of the proton inside the macrobicyclic cavity which results in a very efficient hydrogen-bond network. The present paper, based on previously reported X-ray crystal structures regarding five-atoms bridging units and on molecular modelling studies shows that the disposition of the five donor atoms in the monoprotonated species is related to the protonation site. Precisely, if the protonation occurs on a bridge-head nitrogen the resulting geometry of the donors is a trigonal bipyramid, whereas it is square pyramidal when the proton is bound to a nitrogen belonging to a macrobicyclic chain. For what concerns the geometrical array of the donor atoms in the free amines, the favoured array seems to be the trigonal bipyramidal.     

The shape of the halogen atom—anisotropy of electron distribution and its dependence on basis set and method used

A search through Crystal Structure Database was performed and the distances in contacts of X···N,O, X···H(N,O), and X···C type were collected together with the information on spatial arrangement of the interacting fragments. A detailed statistical analysis showed that the shape of the halogen atom cannot be simply concluded on the basis of interatomic distances in crystal state although originally the concept of anisotropic charge distribution around halogen nuclei was postulated on the basis of such an analysis. It was proven that the conclusions in that case strongly depend on the type of center interacting with the halogen atom. Therefore, it was postulated that the shape of the halogen atom can be estimated for the unperturbed (due to intermolecular interactions) halogen atom. For this purpose, a method was provided to make possible a numerical quantification of the anisotropy of the halogen atom on the basis of electron density measurements performed within the framework of Atoms in Molecules Quantum Theory. The anisotropy of Cl and Br atoms in H₃C–X and F₃C–X (X=Cl, Br) was estimated for MP2 and DFT-B3LYP methods and several different basis sets. The influence of the method and the basis set on the degree of anisotropic distribution of electron density around halogen nuclei was discussed.     

Multi-residue enantiomeric analysis of pharmaceuticals and their active metabolites in the Guadalquivir River basin (South Spain) by chiral liquid chromatography coupled with tandem mass spectrometry

This paper describes the development and application of a multi-residue chiral liquid chromatography coupled with tandem mass spectrometry method for simultaneous enantiomeric profiling of 18 chiral pharmaceuticals and their active metabolites (belonging to several therapeutic classes including analgesics, psychiatric drugs, antibiotics, cardiovascular drugs and β-agonists) in surface water and wastewater. To the authors’ knowledge, this is the first time an enantiomeric method including such a high number of pharmaceuticals and their metabolites has been reported. Some of the pharmaceuticals have never been studied before in environmental matrices. Among them are timolol, betaxolol, carazolol and clenbuterol. A monitoring programme of the Guadalquivir River basin (South Spain), including 24 sampling sites and five wastewater treatment plants along the basin, revealed that enantiomeric composition of studied pharmaceuticals is dependent on compound and sampling site. Several compounds such as ibuprofen, atenolol, sotalol and metoprolol were frequently found as racemic mixtures. On the other hand, fluoxetine, propranolol and albuterol were found to be enriched with one enantiomer. Such an outcome might be of significant environmental relevance as two enantiomers of the same chiral compound might reveal different ecotoxicity. For example, propranolol was enriched with S(?)-enantiomer, which is known to be more toxic to Pimephales promelas than R(+)-propranolol. Fluoxetine was found to be enriched with S(+)-enantiomer, which is more toxic to P. promelas than R(?)-fluoxetine.     

Synthesis and characterisation of PEG-peptide surfaces for proteolytic enzyme detection

Peptide surfaces were obtained by the covalent immobilisation of fluorescently labelled pentapeptides carboxyfluorescein–glycine–arginine–methionine–leucine–glycine, either directly or through a poly(ethylene glycol) (PEG) linker on modified silicon wafers. Each step during the preparation of the peptide surfaces was confirmed by several surface characterisation techniques. Time-of-flight secondary ion mass spectrometry (ToF-SIMS) and X-ray photoelectron spectroscopy were used to determine the surface composition, the wafers philicity was measured by contact angle and atomic force microscopy was used to investigate the surface morphology. Exposure of the peptide surfaces to trypsin resulted in the release of a fluorescently labelled peptide product, which allowed the kinetics of the enzymatic reaction to be followed with the aid of fluorescence spectroscopy. The electrospray ionisation mass spectrometry analysis of the post-digestion solution confirmed that the pentapeptides attached to the solid support undergo specific trypsin hydrolysis at the C-terminus of the arginine residues. Detailed surface analyses before and after the enzyme action was performed using ToF-SIMS. Because of the limited accessibility of the short peptide directly attached to the surface, a quantitative yield of enzymatic hydrolysis was observed only in case when the peptide was bound through the PEG linker. The insertion of the PEG linker increased the number of immobilised peptides and the rate of enzymatic digestion which consequently improved the quality of the enzyme assays. The described approach may be used for different peptide sequences designed for other proteases.

Magnetic resonance study of annealed and rinsed N-doped TiO2 nanoparticles

Nanoparticles of nitrogen-modified TiO₂ (N-doped TiO₂) calcined at 300°C and 350°C, have been prepared with and without water rinsing. Samples were characterized by x-ray diffractrometry (XRD) and optical spectroscopy. The electron paramagnetic resonance (EPR) spectra from centers involving oxygen vacancies were recorded for all samples. These could be attributed to paramagnetic surface centers of the hole type, for example to paramagnetic oxygen radicals O^?, O₂ ^? etc. The concentration of these centers increased after water rising and it further increased for samples annealed at higher temperature. Additionally, for samples calcined at 300°C, and calcined at 350°C and rinsed, the EPR spectra evidenced the presence of magnetic clusters of Ti³⁺ ions. The photocatalytic activity of samples was studied towards phenol decomposition under unltraviolet-visible (UV-Vis) irradiation. It was found that, in comparison to the starting materials, the rinsed materials showed increased photocatalytic activity towards phenol oxidation. The light absorption (UV-Vis/DRS) as well as surface Fourier transform infrared/diffuse reflectance spectroscopy (FTIR/DR) studies confirmed a significantly enhanced light absorption and the presence of nitrogen groups on the photocatalysts surfaces, respectively. A significant increase of concentration of paramagnetic centers connected with oxygen vacancies after water rising has had an essential influence on increasing their photocatalytic activity.      

Bis(diisopropylammonium) thiosulfate and bis(tert‐butylammonium) thiosulfate

Two new dialkylammonium thiosulfates, namely bis(diisopropylammonium) thiosulfate, 2C₆H₁₆N⁺·S₂O₃²⁻, (I), and bis(tert‐butylammonium) thiosulfate, 2C₄H₁₂N⁺·S₂O₃²⁻, (II), have been characterized. The secondary ammonium salt (I) crystallizes with Z = 4, while the primary ammonium salt (II), with more hydrogen‐bond donors, crystallizes with Z = 8 and a noncrystallographic centre of inversion. In both salts, the organic cations and thiosulfate anions are linked within extensive N—H...O and N—H...S hydrogen‐bond networks, forming extended two‐dimensional layers. Layers are parallel to (10) in (I) and to (002) in (II), and have a polar interior and a nonpolar hydrocarbon exterior. The layered structure and hydrogen‐bond motifs observed in (I) and (II) are similar to those in related ammonium sulfates.     

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.     

Identification of Ros Produced by Photodynamic Activity of Chlorophyll/Cyclodextrin Inclusion Complexes

Photodynamic therapy (PDT) is a way of treating malignant tumors and hyperproliferative diseases. It is based on the use of photosensitizer, herein the chlorophyll a (chl a), and a light of an appropriate wavelength. The interaction of the photosensitizer (PS) with the light produces reactive oxygen species (ROS), powerful oxidizing agents, which cause critical damage to the tissue. To solubilize chl a in aqueous solution and to obtain it as monomer, we have used cyclodextrins, carriers which are able to interact with the pigment and form the inclusion complex. The aim of this study is to examine which types of ROS are formed by Chl a/cyclodextrin complexes in phosphate buffered solution and cell culture medium, using specific molecules, called primary acceptors, which react selectively with the reactive species. In fact the changes of the absorption and the emission spectra of these molecules after the illumination of the PS provide information on the specific ROS formation. The ¹O₂ formation has been tested using chemical methods based on the use of Uric Acid (UA), 9,10‐diphenilanthracene (DPA) and Singlet oxygen sensor green (SOSG) and by direct detection of Singlet Oxygen (¹O₂) luminescence decay at 1270 nm. Moreover, 2,7‐dichlorofluorescin and ferricytochrome c (Cyt Fe³⁺) have been used to detect the formation of hydrogen peroxide and superoxide radical anion, which reduces Fe³⁺ of the ferricytochrome to Fe²⁺, respectively.     

New azaphilones from Chaetomium globosum isolated from the built environment

A strain of Chaetomium globosum (DAOM 240359) was isolated from an indoor air sample in Ottawa, Ontario, Canada. When fermented in liquid culture, this strain produced a number of known metabolites including chaetoglobosins A (6), C, and F (7), chaetomugilin D (5), chaetoviridin A (4), and three new nitrogenous azaphilones; 4′-epi-N-2-hydroxyethyl-azachaetoviridin A (1), N-2-butyric-azochaetoviridin E (2), and isochromophilone XIII (3). The structures were elucidated by spectroscopic analysis including; HRMS, 1D and 2D NMR, UV, and ORD. Compounds 2–7 were antimicrobial when tested using quantitative growth inhibition assays.     

Radionuclides and heavy metal concentrations as complementary tools for studying the impact of industrialization on the environment

The aim of the study was to determine whether using chemical and radiochemical analysis of lake sediments can highlight changes in the climate. Also it was studied whether human impact on the environment can be observed and to what extent such changes are in agreement with historical data. Samples of 16 cm thick sediment cores from the Smreczynski Staw Lake were collected and divided into 1 cm thick sub-samples. The samples were air dried and homogenized. The quantitative analysis of Fe, Mn, Zn, Cr, Cu, Ni, Cd, and Pb in the digested sediment samples was made by using atomic absorption spectrometry. Simultaneously, the radioactivity of ¹³⁷Cs using gamma spectrometry and ²¹⁰Pb_uns using alpha spectrometry, were measured for sediment layer dating. Results showed that iron concentration was in the range 0.3–over 1 % (w/w), and zinc 0.01–0.05 % (w/w). Lesser concentrations were found for copper 18.37–43.6 ppm, manganese 37.5–50.7 ppm, lead 146.1–432 ppm, chromium 12.3–37.4 ppm, nickel 3.1–10.8 ppm and cadmium 0.9–34.6 ppm. Changes in ¹³⁷Cs radioactivity was in the range of 89 ± 11 to 865 ± 62 (Bq kg^?1). Sediments composition can accurately reflect (in terms of time and to what extent) air pollution and natural geo-chemical processes in the environment. However, the choice of the analysed object is crucial in this respect. The Smreczynski Staw Lake, due to its location in the mountains and hydrological situation, proved to be very useful for providing undisturbed analytical samples.