Essential oil extraction,chemical analysis and anti-Candida activity of Foeniculum vulgare Miller – new approaches

A comprehensive study on essential oil samples of Foeniculum vulgare Miller from Tarquinia (Italy) is reported. A 24-h systematic steam distillation was performed on different harvested samples applying different extraction times. The GC-MS analysis of the residue outcome showed o-cymene, α-phellandrene, α-pinene and estragole as the major constituents. The predominance and continued presence of o-cymene makes this fennel oil a rather unique chemotype. An evident correlation between the antifungal activity and phenological stage is demonstrated. The most active fractions were particularly rich in estragole, as well as a significant amount of fenchone that possibly exerts some additive effect in the expression of overall antifungal potency. Pre-fruiting material produced oil particularly rich in o-cymene. With reference to the duration of the extraction, the maximum amount of oil was released within the first 3 h, whereas the reproductive phase material needed at least 6 h for the extraction.     

Chemical promenades: Exploring potential-energy surfaces with immersive virtual reality

The virtual-reality framework AVATAR (Advanced Virtual Approach to Topological Analysis of Reactivity) for the immersive exploration of potential-energy landscapes is presented. AVATAR is based on modern consumer-grade virtual-reality technology and builds on two key concepts: (a) the reduction of the dimensionality of the potential-energy surface to two process-tailored, physically meaningful generalized coordinates, and (b) the analogy between the evolution of a chemical process and a pathway through valleys (potential wells) and mountain passes (saddle points) of the associated potential energy landscape. Examples including the discovery of competitive reaction paths in simple A + BC collisional systems and the interconversion between conformers in ring-puckering motions of flexible rings highlight the innovation potential that augmented and virtual reality convey for teaching, training, and supporting research in chemistry.     

Comprehensive model of electromigrative transport in microfluidic paper based analytical devices

A complete mathematical model for electromigration in paper-based analytical devices is derived, based on differential equations describing the motion of fluids by pressure sources and EOF, the transport of charged chemical species, and the electric potential distribution. The porous medium created by the cellulose fibers is considered like a network of tortuous capillaries and represented by macroscopic parameters following an effective medium approach. The equations are obtained starting from their open-channel counterparts, applying scaling laws and, where necessary, including additional terms. With this approach, effective parameters are derived, describing diffusion, mobility, and conductivity for porous media. While the foundations of these phenomena can be found in previous reports, here, all the contributions are analyzed systematically and provided in a comprehensive way. Moreover, a novel electrophoretically driven dispersive transport mechanism in porous materials is proposed. Results of the numerical implementation of the mathematical model are compared with experimental data, showing good agreement and supporting the validity of the proposed model. Finally, the model succeeds in simulating a challenging case of free-flow electrophoresis in paper, involving capillary flow and electrophoretic transport developed in a 2D geometry.     

Unusual nitration of substituted 7-amino-1,8-naphthyridine in the synthesis of compounds with antiplatelet activity

Several 1,8-naphthyridine derivatives have been diazotizated to obtain the corresponding hydroxy derivatives or mixture of hydroxy and hydroxy nitro derivatives. The respective amounts of hydroxy and hydroxy nitro derivatives depends on the nature of the substituents, on their position on the naphthyridine nucleus, on the amount of sodium nitrite and on the reaction temperature. A study of the electronic density of some molecules suggests a possible explanation of the effects induced by the nature of the substituents and of their position. Some of the compounds were tested for their ability to inhibit human platelet aggregation in vitro induced by arachidonic acid. Only compound 26 showed interesting antiplatelet activity.     

Lanthanide-based NMR: a tool to investigate component distribution in mixed-monolayer-protected nanoparticles

Gd(3+) ions, once bound to the monolayer of organic molecules coating the surface of gold nanoparticles, produce a paramagnetic relaxation enhancement (PRE) that broadens and eventually cancels the signals of the nuclear spins located nearby (within 1.6 nm distance). In the case of nanoparticles coated with mixed monolayers, the signals arising from the different coating molecules experience different PRE, depending on their distance from the binding site. As a consequence, observation of the signal broadening patterns provides direct information on the monolayer organization.     

A Combined Experimental and Theoretical Study on the Stereodynamics of Monoaza[5]helicenes: Solvent‐Induced Increase of the Enantiomerization Barrier in 1‐Aza‐[5]helicene

Helicenes and heterohelicenes are attractive compounds with great potential in materials sciences to be used in optoelectronics as ligand backbones in enantioselective catalysis and as chiral sensors. The properties of these materials are related to the stereodynamics of these helical chiral compounds. However, little is known about features controlling stereodynamics in helicenes; in particular, for heterohelicenes the position of the heteroatom could be relevant in this respect. Herein the complete stereodynamic characterization of monoaza[5]helicenes is shown by enantioselective dynamic HPLC and DFT calculations. At variance with previous theoretical calculations, 1‐aza[5]helicene shows a surprisingly high enantiomerization barrier, which is triggered by specific solvent interactions.     

Buckycatcher polymer versus fullerene‐buckycatcher complex: Which is stronger?

The C₆₀H₂₈ buckycatcher (BC) is an excellent host for fullerenes. This receptor features two corannulene pincers which trap C₆₀/C₇₀ via π stacking interactions. Although, the formation of C₆₀@C₆₀H₂₈ complexes is readily observed, the dimerization of C₆₀H₂₈ is not a competitive process, even at high concentrations. By means of first principle calculations, we have studied the thermodynamics of the polymerization of BCs and the formation of fullerene complexes. The results obtained with the M06‐2X, B97‐D, B3LYP‐D3BJ, PBE‐D2, and PBE‐D3 functionals indicated that the interaction energy of (C₆₀H₂₈)₂ is larger than the one computed for C₆₀@C₆₀H₂₈, by 8–10 kcal/mol. Because of the greater number of atoms, and due to the presence of more hydrogens, the inclusion of free energy corrections lowers the energetic separation between (C₆₀H₂₈)₂ and C₆₀@C₆₀H₂₈, even though the dimer maintains its position as being slightly more bound than that of the C₆₀@C₆₀H₂₈. Our calculations indicated that up to the C₆₀H₂₈ trimer could be formed with a free energy change larger than that corresponding to the dimerization and fullerene complexation processes. Finally, we found that the inversion of the corannulene pincers attached to the cyclooctatetraene core is 2–3 kcal/mol lower than that corresponding to free corannulene. We expect that this work can motivate new investigations that may lead to the observation of C₆₀H₂₈ polymers. © 2015 Wiley Periodicals, Inc.     

Thermal lens spectrometric determination of hexavalent chromium

The applicability of thermal lens spectrometry (TLS) for quantification and routine determination of hexavalent chromium was investigated by using a collinear dual beam thermal lens spectrometer. In aqueous solutions the LOD of 0.1 μg l⁻¹ was obtained for Cr(VI) by using 160 mW laser power. The performance of the technique was verified by the determination of hexavalent chromium in standard reference water samples (NIST SRM 1643a and NIST SRM 1643c) and comparing the results for Cr(VI) in CCA (Cr, Cu, As)-treated timber extracts to concentrations obtained by atomic absorption spectrometry (AAS). Good agreement between the TLS results and reported values for Cr(VI) in SRMs as well as AAS results for Cr(VI) in CCA-treated timbers confirmed that TLS is a reliable and accurate analytical technique applicable for the determination of Cr(VI) in aqueous solutions at concentration levels 0.5–100 μg l⁻¹.     

Fast folding and comparison of RNA secondary structures

Summary Computer codes for computation and comparison of RNA secondary structures, the Vienna RNA package, are presented, that are based on dynamic programming algorithms and aim at predictions of structures with minimum free energies as well as at computations of the equilibrium partition functions and base pairing probabilities.An efficient heuristic for the inverse folding problem of RNA is introduced. In addition we present compact and efficient programs for the comparison of RNA secondary structures based on tree editing and alignment.All computer codes are written in ANSI C. They include implementations of modified algorithms on parallel computers with distributed memory. Performance analysis carried out on an Intel Hypercube shows that parallel computing becomes gradually more and more efficient the longer the sequences are.

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Schnelle Faltung und Vergleich von Sekundärstrukturen von RNA

Zusammenfassung Die im Vienna RNA package enthaltenen Computer Programme für die Berechnung und den Vergleich von RNA Sekundärstrukturen werden präsentiert. Ihren Kern bilden Algorithmen zur Vorhersage von Strukturen minimaler Energie sowie zur Berechnung von Zustandssumme und Basenpaarungswahrscheinlichkeiten mittels dynamischer Programmierung.Ein effizienter heuristischer Algorithmus für das inverse Faltungsproblem wird vorgestellt. Darüberhinaus präsentieren wir kompakte und effiziente Programme zum Vergleich von RNA Sekundärstrukturen durch Baum-Editierung und Alignierung.Alle Programme sind in ANSI C geschrieben, darunter auch eine Implementation des Faltungs-algorithmus für Parallelrechner mit verteiltem Speicher. Wie Tests auf einem Intel Hypercube zeigen, wird das Parallelrechnen umso effizienter je länger die Sequenzen sind.