On geometries of stacked and H-bonded nucleic acid base pairs determined at various DFT, MP2, and CCSD(T) levels up to the CCSD(T)/complete basis set limit level

The geometries and interaction energies of stacked and hydrogen-bonded uracil dimers and a stacked adeninecdots, three dots, centeredthymine pair were studied by means of high-level quantum chemical calculations. Specifically, standard as well as counterpoise-corrected optimizations were performed at second-order Moller-Plesset (MP2) and coupled cluster level of theory with single, double, and perturbative triple excitations [CCSD(T)] levels with various basis sets up to the complete basis set limit. The results can be summarized as follows: (i) standard geometry optimization with small basis set (e.g., 6-31G(*)) provides fairly reasonable intermolecular separation; (ii) geometry optimization with extended basis sets at the MP2 level underestimates the intermolecular distances compared to the reference CCSD(T) results, whereas the MP2/cc-pVTZ counterpoise-corrected optimization agrees well with the reference geometries and, therefore, is recommended as a next step for improving MP2/cc-pVTZ geometries; (iii) the stabilization energy of stacked nucleic acids base pairs depends considerably on the method used for geometry optimization, so the use of reliable geometries, such as counterpoise-corrected MP2/cc-pVTZ ones, is recommended; (iv) the density functional theory methods fail completely in locating the energy minima for stacked structures and when the geometries from MP2 calculations are used, the resulting stabilization energies are strongly underestimated; (v) the self-consistent charges-density functional tight binding method, with inclusion of the empirical dispersion energy, accurately reproduces interaction energies and geometries of dispersion-bonded (stacked) complexes; this method can thus be recommended for prescanning the potential energy surfaces of van der Waals complexes.     

Zwitterionic ion chromatography with carboxybetaine surfactant-coated particle packed and monolithic type columns

Both particle packed (25 cm x 0.46 cm I.D. SUPELCOSIL 5 microm C18) and monolithic type (10 cm x 0.46 cm I.D. Merck Chromolith Performance C18) reversed-phase substrates were dynamically coated with a carboxybetaine type zwitterionic surfactant ((dodecyldimethyl-amino) acetic acid) and investigated as stationary phases for use in zwitterionic ion chromatography (ZIC). Investigations into eluent concentration and pH were carried out using KCl eluents containing 0.2 mM of the carboxybetaine surfactant to stabilise the column coatings. It was found that eluent concentration decreased anion retention whilst simultaneously increasing peak efficiencies, which may be due to the dissociation of intra- and inter-molecular salts of the carboxybetaine surfactant under higher ionic strength conditions. The Effect of eluent pH was an increase in anion retention with decreased eluent pH due to the increased protonation of the weak acid terminal group of the carboxybetaine, causing both a relative increase in the positive charge of the stationary phase and less repulsion of the anions by the dissociated weak acid group. The carboxybetaine-coated monolithic phase was applied to rapid anion separations using elevated flow rates and flow rate gradients.     

[2 + 2] Photodimerization of the acenaphthylene ruthenium complex [(C5Me4CH2OMe)Ru(η6-C12H8)]+

The [2 + 2] photodimerization of the complex [(C₅Me₄CH₂OMe)Ru(η⁶-C₁₂H₈)]⁺ under visible-light irradiation leads to a mixture of the head-to-head heptacyclene products [(μ-η⁶: η⁶-C₂₄H₁₆)Ru₂(C₅Me₄CH₂OMe)₂]²⁺ (syn- and anti-) with the predominant formation of the syn-isomer; the structures of both isomers were established by X-ray diffraction analysis.     

Synthesis of New Heteroatomic Podands from Ethyl 2-[(2-Aminophenylamino)Methylidene]-3-Oxoalkanoates and Thiophene-2,5-Dicarboxaldehyde

Condensation of two moles of ethyl 2-[(2-aminophenylamino)methylidene]-3-oxo-3-(polyfluoroalkyl)propionates with 2,5-thiophene-dicarboxaldehyde results in new heteroatomic podands. X-ray data showed that in the solid state these molecules arrange in two independent chelating fragments of b-amino enone type, thiophene fragment being a spacer.     

Ultrathin functional films of titanium(IV) oxide

Chemistry and physics of thin semiconducting layers of various types are subjects of intense research. Especially when nanotechnology methods such as self-assembly are involved, amazing structural and/or functional properties may appear. Also modern physical methods using variously organized plasma arrangements are able to produce uniform structures with distinctive functionality. In this review, based virtually on our own work, discussions on the preparation, structure, morphology, and function of titanium(IV) oxide nanoscopic thin films are presented. It was shown that structurally and functionally similar titanium(IV) oxide films can be prepared via completely different preparation techniques. Function tests were arranged as “primary”, covering the assessment of the light induced charge separation efficiency, and “secondary”, based on photocatalytic surface oxidations.     

Biosynthesis of Quantum Dots (CdTe) and its Effect on Eisenia fetida and Escherichia coli

Biosynthesis belongs to one of the new possibilities of nanoparticles preparation, whereas its main advantage is biocompatibility. In addition, the ability of obtaining the raw material for such synthesis from the soil environment is beneficial and could be useful for remediation. However, the knowledge of mechanisms that are necessary for the biosynthesis or effect on the bio-synthesizing organisms is still insufficient. In this study, we attempted to evaluate the effect of quantum dots (QDs) not only on a model organism of collembolans, but also on another soil organism—earthworm Eisenia fetida—and in also one widespread microorganism such as Escherichia coli. Primarily, we determined 28EC₅₀ as 72.4 μmol L⁻¹ for CdTe QDs in collembolans. Further, we studied the effect of QDs biosynthesis in E. fetida and E. coli. Using determination of QDs, low-molecular thiols and antioxidant activities, we found differences between both organisms and also between ways how they behave in the presence of Cd and/or Cd and Te. The biosynthesis in earthworms can be considered as its own protective mechanism; however, in E. coli, it is probably a by-product of protective mechanisms.

     

Unexpected formation of dinaphthoaza-17-crown-5 ether containing γ-aminopiperidine subunit

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