Modification of micro-crystalline graphite and carbon black by acetone, toluene, and phenol.

The chemical interactions of two types of graphite and two types of carbon black (CB) with acetone, toluene, and phenol were studied in order to evaluate the influence of chemical treatment on the structure and morphology of the carbon phases. The experimental treatment of carbon phases was carried out at room temperature for 1 hour. The chemical and phase composition were studied by x-ray photoelectron (XP) and Raman spectroscopies, while the morphology and structure were determined by powder x-ray diffraction, as well as transmission electron microscopy techniques. To shed light on the most probable explanation of the observed results, we performed simulations and calculations of the binding energies of acetone, toluene, and phenol with model carbon phases: a perfect graphene sheet and a defective graphene sheet containing various structural defects (vacancies as well as zigzag and armchair edges). Simulations show that all non-covalent and most covalent coupling reactions are exothermic, with acetone coupling having the higher calorimetric effect. Based on the results of the simulations and the XP spectroscopy measurements, the probable reactions taking place during the respective treatments are outlined. The conducted studies (both theoretical and experimental) show that the treatment of graphite powders and CB with acetone, toluene, or phenol can be used as a preliminary stage of their modification and/or functionalization, including their conversion into graphene-like (defective graphene, reduced graphene oxide, and/or graphene oxide) phases. For example, the treatment of SPHERON 5000 with acetone significantly facilitates their subsequent modification with laser radiation to graphene-like phases.

Sodium and Magnesium Ion Location at the Backbone and at the Nucleobase of RNA: Ab Initio Molecular Dynamics in Water Solution.

The interactions between Na+ or Mg2+ ions with different parts of single-stranded RNA molecules, namely, the oxygen atoms from the phosphate groups or the guanine base, in water solution have been studied using first-principles molecular dynamics. Sodium ions were found to be much more mobile than Mg2+ ions and readily underwent transitions between a state directly bonded to RNA oxygen atoms and a completely solvated state. The inner solvation shell of Na+ ions fluctuated stochastically at a femtosecond timescale coordinating on average 5 oxygen atoms for bonded Na+ ions and 5.5 oxygen atoms for solvated Na+ ions. In contrast, the inner solvation shell of Mg2+ ions was stable in both RNA-bonded and completely solvated states. In both cases, Mg2+ ions coordinated 6 oxygen atoms from the inner solvation shell. Consistent with their stable solvation shells, Mg2+ ions were more effective than Na+ ions in stabilizing the RNA backbone conformation. The exclusion zones between the first and second solvation shells, solvation shell widths, and angles for binding to carbonyl oxygen of guanine for solvated Na+ or Mg2+ ions exhibited a number of quantitative differences when compared with RNA crystallographic data. The presented results support the distinct capacity of Mg2+ ions to support the RNA structure not only in the crystal phase but also in the dynamic water environment both on the side of the phosphate moiety and on the side of the nucleobase.

Interaction of Na+, K+, Mg2+ and Ca2+ counter cations with RNA.

Alkaline and alkaline earth ions, namely Na+, K+, Mg2+ and Ca2+, are critical for the stability, proper folding and functioning of RNA. Moreover, those metal ions help to facilitate macromolecular interactions as well as the formation of supramolecular structures (e.g. the ribosome and the ribozymes). Therefore, identifying the interactions between ions and nucleic acids is a key to the better comprehension of the physical nature and biological functions of those biomolecules. The scope of this review is to highlight the preferential location and binding sites of alkaline and alkaline earth metal ions compensating the negatively charged backbone of nucleic acids and interacting with other electronegative centers, focusing on RNA. We summarize experimental studies from X-ray crystallography and spectroscopic analysis (infrared, Raman and NMR spectroscopies). Computational results obtained with classical and ab initio methods are presented afterwards.