Predicting the Limit of Intramolecular Hydrogen Bonding with Classical Molecular Dynamics

The energetics of intramolecular recognition processes are governed by the balance of pre‐organization and flexibility, which is often difficult to measure and hard to predict. Using classical MD simulations, we predict and quantify the effective strength of intramolecular hydrogen bonds between donor and acceptor sites separated by a variable alkyl linker in several solvents and crowded solutions. The balance of entropic and enthalpic contributions poses a solvent‐dependent limit to the occurrence of intramolecular H‐bonding. Still, free energies show a constant offset among different solvents with, for example, a 13 kJ mol^?1 difference between water and chloroform. Molecular crowding shows little effect on the thermodynamic equilibrium, but induces variations on the H‐bond kinetics. The results are in quantitative agreement with experiments in chloroform and showcase a general strategy to investigate molecular interactions in different environments, extending the limits of current experiments towards the prospective prediction of H‐bond interactions in a variety of contexts.     

Influence of Defects on the Stability and Hydrogen-Sorption Behavior of Mg-Based Hydrides

This review deals with the destabilization methods for improvement of storage properties of metal hydrides. Both theoretical and experimental approaches were used to point out the influence of various types of defects on structure and stability of hydrides. As a case study, Mg, and Ni based hydrides has been investigated. Theoretical studies, mainly carried out within various implementations of DFT, are a powerful tool to study mostly MgH₂ based materials. By providing an insight on metal-hydrogen bonding that governs both thermodynamics and hydrogen kinetics, they allow us to describe phenomena to which experimental methods have a limited access or do not have it at all: to follow the hydrogen sorption reaction on a specific metal surface and hydrogen induced phase transformations, to describe structure of phase boundaries or to explain the impact of defects or various additives on MgH₂ stability and hydrogen sorption kinetics. In several cases theoretical calculations reveal themselves as being able to predict new properties of materials, including the ways to modify Mg or MgH₂ that would lead to better characteristics in terms of hydrogen storage. The influence of ion irradiation and mechanical milling with and without additives has been discussed. Ion irradiation is the way to introduce a well-defined concentration of defects (Frankel pairs) at the surface and sub-surface layers of a material. Defects at the surface play the main role in sorption reaction since they enhance the dissociation of hydrogen. On the other hand, ball-milling introduce defects through the entire sample volume, refine the structure and thus decrease the path for hydrogen diffusion. Two Severe Plastic Deformation techniques were used to better understand the hydrogenation/dehydrogenation kinetics of Mg- and Mg₂Ni-based alloys: Equal-Angular-Channel-Pressing and Fast-Forging. Successive ECAP passes leads to refinement of the microstructure of AZ31 ingots and to instalment therein of high densities of defects. Depending on mode, number and temperature of ECAP passes, the H-sorption kinetics have been improved satisfactorily without any additive for mass H-storage applications considering the relative speed of the shaping procedure. A qualitative understanding of the kinetic advanced principles has been built. Fast-Forging was used for a “quasi-instantaneous” synthesis of Mg/Mg₂Ni-based composites. Hydrogenation of the as-received almost bi-phased materials remains rather slow as generally observed elsewhere, whatever are multiple and different techniques used to deliver the composite alloys. However, our preliminary results suggest that a synergic hydrogenation / dehydrogenation process should assist hydrogen transfers from Mg/Mg₂Ni on one side to MgH₂/Mg₂NiH₄ on the other side via the rather stable a-Mg₂NiH_0.3, acting as in-situ catalyser.     

Surface polymerization by ion-assisted deposition for polythiophene film growth

Cationic polymerization is induced at the gas-solid interface by hyperthermal organic cations coincident on a surface with a thermal beam of organic monomers. This process, termed surface polymerization by ion-assisted deposition (SPIAD), produces films that maintain the chemical structure of the monomer. A polythiophene film is produced here by SPIAD with 100 eV thiophene ions and terthiophene monomers coincident on Si and indium tin oxide (ITO) substrates held under vacuum. X-ray photoelectron spectroscopy observes enhancement in film growth for SPIAD compared with either thiophene ion or terthiophene exposure alone. Polythiophene films grown by both mass-selected and nonmass-selected ions with coincident terthiophene dosing both display similar fluorescence intensities at two wavelengths characteristic of emission from films of the terthiophene monomer. Raman spectra of films from nonmass-selected ions display several vibrations also observed in terthiophene films. Ions therefore play a critical role in film growth from nonmass-selected ions, in addition to any radical or photochemically driven processes that may also occur.     

Growth of novel polythiophene and polyphenyl films via surface polymerization by ion-assisted deposition

Surface polymerization by ion-assisted deposition (SPIAD) is used here to grow novel polythiophene and polyphenyl thin films on a silicon surface by hyperthermal, mass-selected thiophene cations coincident with a thermal beam of alpha-terthiophene or p-terphenyl neutrals. X-ray photoelectron spectroscopy (XPS) observes a large enhancement in film growth for SPIAD compared with either thiophene ions or alpha-terthiophene exposure alone. Changes in S/Si and C/Si ratios from XPS, direct observation of higher polymerization products by mass spectrometry, characteristic vibrations in the Raman data, and enhanced stability in a vacuum all indicate that 200 eV SPIAD polythiophene films are most efficiently polymerized at a 1/150 ion/neutral ratio. Other ion/neutral ratios are less efficient at film growth, in the order 1/150 > 1/450 > 1/900 > direct ion deposition > 1/50. Changes in C/Si ratios and higher polymerization products indicate polymerization occurs in SPIAD polyphenyl films grown with a 1/100 ion/neutral ratio. Furthermore, thiophene ions are found to incorporate into some, but not all, of the polymerization products observed in mass spectrometry.     

Technetium removal from the aqueous solution using zeolites A and Y containing transition metal ions Co2+ and Zn2+

Journal of Radioanalytical and Nuclear Chemistry - The adsorption properties of two zeolite types, faujasite (NaY, ZnY, CoY) and LTA-4A zeolite (NaA, ZnA, CoA), towards technetium were studied in...     

Assessment of heavy metals pollution in Sudanese harbours along the Red Sea Coast

The levels of some heavy metals in sediments of two harbours along the Sudanese Coast of the Red Sea were examined and reported for the first time. A total of thirty-six surface sediment samples were collected from Port-Sudan and Sawakin harbours. Part of each sample was partitioned into five fractions with grain-size ranges of 1000–500, 500–250, 250–125, 125–63 and less than 63 μm. The Mn, Fe, Ni, Cu, Zn and Pb concentration in bulk samples and sub-samples were determined by atomic absorption spectrophotometry. The spatial distribution pattern of heavy metal content of crustal origin in the sediments is more uniform in Port-Sudan harbour than in Sawakin harbour. The granulometric normalization revealed that some sites in Port-Sudan harbour and one site in Sawakin harbour have been exposed to different levels of heavy metal contamination, which probably originated from ships, industrial and domestic activities.     

Discovery of new therapeutic targets by the informational spectrum method

The field of bioinformatics has become a major part of the drug discovery pipeline playing a key role in improvement and acceleration of this time and money consuming process. Here we review the application of the informational spectrum method (ISM), a virtual spectroscopy method for structure/function analysis of proteins, in identification of functional protein domains representing candidate therapeutic targets for drugs against human immunodeficiency virus (HIV)-1, anthrax, highly pathogenic influenza virus H5N1 and cardiovascular diseases.     

Structural Characterization,Antimicrobial Activity and BSA/DNA Binding Affinity of New Silver(I) Complexes with Thianthrene and 1,8-Naphthyridine

Three new silver(I) complexes [Ag(NO₃)(tia)(H₂O)]_n (Ag1), [Ag(CF₃SO₃)(1,8-naph)]_n (Ag2) and [Ag₂(1,8-naph)₂(H₂O)_1.2](PF₆)₂ (Ag3), where tia is thianthrene and 1,8-naph is 1,8-naphthyridine, were synthesized and structurally characterized by different spectroscopic and electrochemical methods and their crystal structures were determined by single-crystal X-ray diffraction analysis. Their antimicrobial potential was evaluated against four bacterial and three Candida species, and the obtained results revealed that these complexes showed significant activity toward the Gram-positive Staphylococcus aureus, Gram-negative Pseudomonas aeruginosa and the investigated Candida species with minimal inhibitory concentration (MIC) values in the range 1.56–7.81 μg/mL. On the other hand, tia and 1,8-naph ligands were not active against the investigated strains, suggesting that their complexation with Ag(I) ion results in the formation of antimicrobial compounds. Moreover, low toxicity of the complexes was detected by in vivo model Caenorhabditis elegans. The interaction of the complexes with calf thymus DNA (ct-DNA) and bovine serum albumin (BSA) was studied to evaluate their binding affinity towards these biomolecules for possible insights into the mode of antimicrobial activity. The binding affinity of Ag1–3 to BSA was higher than that for DNA, indicating that proteins could be more favorable binding sites for these complexes in comparison to the nucleic acids.     

Tissue-protective effects of fullerenol C60(OH)24 and amifostine in irradiated rats

Polyhydroxylated fullerenes, named fullerenols (C(60)(OH)(n); n=12-26) are excellent antioxidants. Harmful effects of ionizing radiation on living organism are mainly mediated by free radical species and fullerenols attract an attention as a potential radioprotectors. Our preliminary investigations on mice and rats subjected to radiation injury show that fullerenol C(60)(OH)(24) provides high survival rate of irradiated small rodents. Radioprotective effect was comparable to that of the standard radioprotector amifostine. The aim of this study was to compare the efficacy of fullerenol C(60)(OH)(24) (10 and 100mg/kg i.p.) and amifostine (300 mg/kg i.p.) in protection of rats against harmful effects of ionizing radiation. The animals were whole-body irradiated by X-rays (8 MV). Both compounds were given 30 min before irradiation. In order to evaluate the general radioprotective efficacy of fullerenol and amifostine rats were irradiated with an absolutely lethal dose of X-rays (8 Gy) and their survival and body mass gain were monitored during the period of 30 days after irradiation. The aim of the second part of the study is to investigate the tissue-protective effects of tested compounds (100 mg/kg i.p. of fullerenol and 300 mg/kg i.p. of amifostine, 30 min before irradiation). It was carried out on rats irradiated with a sublethal dose of X-rays (7 Gy). Influence of ionizing radiation on hematopoesis as well as the radioprotective efficiency of the compounds given were evaluated by determining blood cell count during 28 days after irradiation. For this purpose the blood was taken from tail vein before irradiation and on the 3rd, 7th, 14th, 21st and 28th day after irradiation. In order to estimate the radioprotective effects of fullerenol and amifostine on other rat tissue, the animals were sacrificed on the 7th and 28th day after irradiation and their main organs (lung, heart, liver, kidney, small intestine and spleen) were taken for histopathological analysis. In the experiment in which the general radioprotective efficacy of fullerenol and amifostine was examined, fullerenol given in a dose of 100mg/kg produced better protection than given in a dose of 10mg/kg. This effect was comparable to that of amifostine. The results of hematological investigations showed that fullerenol better than amifostine prevented radiation-induced reduction in the white cell count (granulocytes and lymphocytes), particularly in the first 7 days after irradiation. Pathohistology examinations revealed better radioprotective effects of fullerenol compared to those of amifostine on the spleen, small intestine and lung, while amifostine had better radioprotective effects than fullerenol in protection of the heart, liver and kidney. These results confirm satisfactory radioprotective efficacy of fullerenol and encourage further investigations as a potential radioprotector.     

Rapid headspace solid-phase microextraction-gas chromatographic-time-of-flight mass spectrometric method for qualitative profiling of ice wine volatile fraction. I. Method development and optimization

An analytical method for the determination of volatile and semi-volatile compounds representing various chemical groups in ice wines was developed and optimized in the presented study. A combination of the fully automated solid-phase microextraction (SPME) sample preparation technique and gas chromatographic-mass spectrometric (GC-MS) system to perform the final chromatographic separation and identification of the analytes of interest was utilized. A time-of-flight mass spectrometric (TOF-MS) analyzer provided very rapid analysis of this relatively complex matrix. Full spectral information in the range of m/z 35-450 was collected across the short GC run (less than 5 min). Divinylbenzene/Carboxen/Polydimethylsiloxane (DVB/CAR/PDMS) 50/30 microm fiber performed best during the optimization experiments and it was used in the headspace SPME mode to isolate compounds from ice wine samples, consisting of 3 mL wine with 1g salt addition. After the sample incubation and extraction (both 5 min at 45 degrees C), analytes were thermally desorbed in the GC injector for 2 min (injector maintained at 260 degrees C) and transferred into the column. The MS data acquisition rate of 50 spectra/s was selected as optimal. The optimized analytical method did not exceed 20 min per sample, including both the isolation and pre-concentration of the analytes of interest, the final GC-TOF-MS analysis and the fiber bake-out. Both a linear temperature-programmed retention index (LTPRI) method using C(8)-C(20) alkanes loaded onto the fiber and a mass spectral library search were employed to identify the target compounds. The repeatability of the developed and optimized HS-SPME-GC-TOF-MS method for ice wine analysis, expressed as relative standard deviation (RSD, %, n=7), ranged from 3.2 to 9.0%.