Method of fast trace microanalysis of the chiral pesticides epoxiconazole and novaluron in soil samples using off-line flow-through extraction and on-column direct large volume injection in reversed-phase high performance liquid chromatography

An analytical method combining off-line flow-through extraction of a soil micro-sample (mass around 100 mg, packed into a short HPLC glass column) and direct on-column large-volume injection (LVI up to 1.00 mL) of a methanol-water soil extract onto a conventional C18 RP HPLC column enabled fast (within 3.5 minutes) trace micro-analysis of the relatively new chiral pesticides epoxiconazole (E) and novaluron (N), respectively. Linear calibration curves were evaluated from UV detection (230 nm) data in the range from 0.1 to 5 mg/kg in three most abundant Slovak agricultural soils. LOD (confidence band) at the levels 0.08-0.11 mg/kg and LOQ 0.4-0.6 mg/kg and LOD (S/N = 3) at the levels 0.007-0.018 mg/kg and LOQ (S/N = 10) 0.024-0.060 mg/kg, respectively, of dry soil were achieved. Recovery of pesticides in the overall LVI method including flow-through 130-200 mg soil micro-sample extraction was: for epoxiconazole from 74 to 85% and from 56% to 90% for novaluron with reproducibility within +/- 6% RSD. This fast (30 min) and simple method consists of just three steps which are short column filling with a solid micro-sample; flow-through liquid extraction and direct large-volume injection RP HPLC DAD analysis. The method is prepared for automation and further analysis of enantiomers of both investigated pesticides by achiral-chiral column switching techniques.     

Conformational structure of some trimeric and pentameric structural units of heparin

The molecular structure of trimeric units (D-E-F and F-G-H) and the pentamer D-E-F-G-H of heparin (sodium salts and their anionic forms) was studied using the B3LYP/6-31G(d) method. The equilibrium structure of the sodium salts of the trimers and pentamer investigated in the isolated state was determined by multidentate coordination of the sodium cations with oxygen atoms of the sulfate, carboxyl, and hydroxyl (hydroxymethyl) groups, respectively. The displacement of Na+ ions from the binding sites in the sodium salt of oligosaccharides studied resulted in the appreciable change of the overall conformation of the corresponding anion. Upon dissociation, a large change in both the position of the sulfate groups and the conformation across the glycosidic bonds was observed. The stable energy conformations around the glysosidic bonds found for the pentamer investigated are compared and discussed with the available experimental X-ray structural data for the structurally related heparin-derived pentasaccharides in cocrystals with proteins.     

Copper cation interactions with biologically essential types of ligands: a computational DFT study

This work presents a systematic theoretical study on Cu(I) and Cu(II) cations in variable hydrogen sulfide-aqua-ammine ligand fields. These ligands model the biologically most common environment for Cu ions. Molecular structures of the complexes were optimized at the density functional theory (DFT) level. Subsequent thorough energy analyses revealed the following trends: (i) The ammine complexes are the most stable, followed by those containing the aqua and hydrogen sulfide ligands, which are characterized by similar stabilization energies. (ii) The most preferred Cu(I) coordination number is 2 in ammine or aqua ligand fields. A qualitatively different binding picture was obtained for complexes with H(2)S ligands where the 4-coordination is favored. (iii) The 4- and 5-coordinated structures belong to the most stable complexes for Cu(II), regardless of the ligand types. Vertical and adiabatic ionization potentials of Cu(I) complexes were calculated. Charge distribution (using the natural population analysis (NPA) method) and molecular orbital analyses were performed to elucidate the nature of bonding in the examined systems. The results provide in-depth insight into the Cu-binding properties and can be, among others, used for the calibration of bioinorganic force fields.     

Algorithm for coding DNA sequences into "spectrum-like" and "zigzag" representations

An algorithm for encoding long strings of building blocks, like 4 DNA bases (adenine-A, cytosine-C, thymine-T, and guanidine-G), 20 natural amino acids (from Alanine Ala to Valine-Val, plus the stop triplet), or all 64 possible base triplets (from AAA to TTT), into "zigzag" or "spectrum-like" representations is suggested. The new encoding scheme can be derived in the 3-, 2-, or 1-dimensional form depending on the user's wishes. The only information, besides the string for which the "spectrum-like" representation is sought, is the initial positioning of the complete set of units from which the string is composed, i.e., four positions for A, C, G, and T, or 20 positions for natural amino acids plus stop, etc. This initial positioning can be initialized in either the 3-, 2-, or 1-D form. As an illustration of the suggested encoding scheme of the visual and chemometric comparison of the first 10 exon strings of the beta globin gene of 10 different species, each string consisting of about 100 basic amino acids long is shown.     

Quantum mechanical study of the potential energy surface of the ClO + NO2 reaction

In the study of the reaction pathways of the ClO + NO2 reaction including reliable structures of the reactants, products, intermediates, and transition states as well as energies the MP2/6-311G(d), B3LYP/6-311G(d), and G2(MP2) methods have been employed. Chlorine nitrate, ClONO2, is formed by N-O association without an entrance barrier and is stabilized by 29.8 kcal mol(-1). It can undergo either a direct 1,3 migration of Cl or OCl rotation to yield an indistinguishable isomer. The corresponding barriers are 45.8 and 7.1 kcal mol(-1), respectively. ClONO2 can further decompose into NO3 + Cl with an endothermicity of 46.4 kcal mol(-1). The overall endothermicity of the NO2 + ClO --> NO3 + Cl reaction is calculated to be 16.6 kcal mol(-1). The formation of cis-perp and trans-perp conformer of chlorine preoxynitrite, ClOONO(cp) and ClOONO(tp), are exothermic by 5.4 and 3.8 kcal mol(-1), respectively. Calculations on the possible reaction pathways for the isomerization of ClOONO to ClONO2 showed that the activation barriers are too high to account for appreciable nitrate formation from peroxynitrite isomerization. All quoted relative energies are related to G2(MP2) calculations.     

Partitioning of <Emphasis Type="Italic">π</Emphasis> -electrons in rings of polycyclic conjugated hydrocarbons: Part 6. Comparison with other methods for estimating the local aromaticity of rings in polycyclic benzenoids

By adopting the convention that shared double bonds in polycyclic conjugated hydrocarbons contribute with one -electron and unshared ones with two -electrons, a partition of -electrons in each ring (-electron content, EC) can be obtained by averaging over all Kekulé structures, which are assumed to have equal weights. This affords a simple measure of local aromaticity that is comparable with other such local aromaticity indices in polycyclic benzenoids.     

Affinity chromatography of porcine pepsin A using quinolin-8-ol as ligand

Stationary phase containing quinolin-8-ol immobilized on macroporous methacrylate support for the affinity chromatography of porcine pepsin A is described. Optimized chromatographic conditions for separation of porcine pepsin A on this stationary phase were found investigating the influence of pH, concentration, ionic strength and chemical composition of the used mobile phases. The stationary phase shows a good reproducibility of chromatographic analyses (relative standard deviation, +/-2%), a high recovery (ca. 93%) and a satisfactory capacity (13 mg pepsin A/1 mL stationary phase) for porcine pepsin A. The obtained findings confirm the applicability of affinity chromatography on the stationary phase with immobilized quinolin-8-ol to the isolation and determination of porcine pepsin A.     

Quadrupole Splitting Distributions in Purpurite and Related Minerals

The quadrupole splitting distributions (QSDs) from the Mössbauer spectra of triphylite, ferrisicklerite and purpurite at 298 K and 80 K were obtained by the use of the Voigt-based quadrupole splitting distribution (QSD) method for the first time. QSDs of Fe²⁺ and Fe³⁺ are attributed to Fe²⁺ and Fe³⁺ at the corresponding octahedrally coordinated sites in the crystal structures of the three phosphate minerals. The influence on the distortion of the M2 site by different next-nearest neighbor (NNN) configurations was discussed based on the Jahn–Teller effect in purpurite, and the authors propose two M2 subsites with different distortions in purpurite. Two QSDs of Fe³⁺ in the Mössbauer spectra of purpurite are tentatively assigned to Fe³⁺ at the two M2 subsites, and next-nearest neighbor (NNN) effects were used to interpret the Mössbauer spectra of purpurite.     

Raman spectroscopic study of the uranyl sulphate mineral zippeite: low wavenumber and U–O stretching regions

The uranyl sulphate mineral zippeite was studied by Raman spectroscopy. The phase purity of the sample was initially checked by X-ray powder diffraction and its chemical composition was defined by electron microprobe (wavelength dispersive spectroscopy, WDS) analysis. The Raman spectroscopy research focused on the low wavenumber and uranyl stretching vibration regions. Vibration bands down to 50 cm^–1 were tentatively assigned. The U–O bond lengths were calculated based on empirical relations. Inferred values are consistent with those obtained from the crystal structure analysis of synthetic zippeite. Number of bands was interpreted on the basis of factor group analysis.     

Photo- and radiation-induced preparation of nanocrystalline copper and cuprous oxide catalysts

Spherical copper nanoparticles have been prepared by photo- or radiation-induced reduction of aqueous solutions containing 10⁻³ mol.dm⁻³ copper sulphate or formate, 1.3 mol.dm⁻³ propan-2-ol and polyvinyl alcohol as a stabilizer. Increase of initial copper concentration to 10⁻² mol.dm⁻³ resulted in formation of different reaction product—octahedral cuprous oxide nanoparticles. Solutions were irradiated by means of electron beam, ⁶⁰Co γ rays (dose rate 70 Gy.h⁻¹) or by 400 W medium-pressure mercury lamp and were characterised by UV-Vis spectrophotometry, X-Ray Powder Diffraction, TEM and SEM. Pink to violet colour of colloidal copper solutions corresponded to measured copper surface plasmon band at circa 580 nm and has been found to be very sensitive to oxygen, which causes dissolution of particles. Therefore, the influence of purging by nitrogen gas prior to irradiation was thoroughly examined and has been found to only hinder, not alter irradiation effects. Moreover, the evolution of absorption spectrum of colloidal copper solution in contact with air has been measured, revealing interesting non-monotonous dependence on the air exposure time, probably caused by formation of protective oxide layer. Catalytic activity of prepared cuprous oxide has been measured by catalytic decomposition of hydrogen peroxide and has been found to be higher or comparable to commercial cuprous oxide.