Intercalating Nucleic Acids Containing Insertions of Naphthalimide

In a study of linker‐length dependence, we evaluated naphthalimide (= 1H‐benzo[de]isoquinoline‐1,3(2H)‐dione) and 4‐bromonaphthalimide as intercalating nucleic acids. We used a vicinal dihydroxy system when incorporating the six different naphthalimide monomers into DNA, and found the minimum linker‐length to be five C‐atoms. With this length of the linker, naphthalimide was discriminating between DNA and RNA – stabilizing DNA, while destabilizing RNA. Furthermore, naphthalimide showed universal base character by hybridizing to the four natural bases with a range as narrow as 1.4°. When compared to pyrene, naphthalimide with the same linker‐length gave significantly higher thermal meltings when hybridized to DNA.     

Rate-equation calculations of the current flow through two-site molecular device and DNA-based junction

Here we present the calculations of incoherent current flowing through the two-site molecular device as well as the DNA-based junction within the rate-equation approach. Selected phenomena of interest are discussed in detail. The structural asymmetry of a two-site molecule results in a rectification effect, which can be neutralized by an asymmetric voltage drop at the molecule-metal contacts due to coupling asymmetry. The results received for the poly(dG)-poly(dC) DNA molecule reveal the coupling-and temperature-independent saturation effect of the current at high voltages, establishing for short chains the inverse square distance dependence. Additionally we document the conductance peak shifting in the direction of higher voltages due to a temperature decrease.     

Synthesis of Monofunctionalized Silsesquioxanes (RSiMe2O)(iBu)7Si8O12 via Alkene Hydrosilylation

The research presented in this work comprehensively describes hydrosilylation of a wide spectrum of alkenes which contain one or more reactive groups with (HSiMe₂O)(iBu)₇Si₈O₁₂, in the presence of different types of catalysts. Special attention is paid to the influence of alkene, catalyst, and reaction conditions on process effectiveness and selectivity by the precise monitoring of the experiments with in situ FTIR and NMR spectroscopies. More than twenty silsesquioxanes bearing reactive groups (OH, Br, NR₂, CO, COOR, NCO, epoxy, SiR₃) commonly used in organic and polymer chemistry, were obtained, isolated and characterized by ¹H, ¹³C, ²⁹Si NMR and MALDI TOF. Importantly, in the presented syntheses, commercially available reagents and catalysts were used, meaning that the presented methods could be easily repeated, rapidly scaled up, and widely applied.     

Analysis of red inks by micellar electrokinetic capillary chromatography with laser‐induced fluorescence detection

A combination of MEKC with a—highly sensitive but not commonly used—LIF detector was tested regarding the possibility of differentiation of red inks. The separation process was conducted in a fused silica capillary (id 50 μm, 60/50 cm total/effective length) in BGE consisting of 40 mM sodium borate, 20 mM SDS and 10% v/v ACN with 30 kV applied. The optimized temperature of storage and capillary was 10 and 25°C, respectively. The samples were prepared using 20 dots (ø 0.5 mm), extracted in 35 μL BGE and diluted with 30 μL of water. The proposed method showed excellent repeatability and reproducibility (RSD (t_m) < 0.8 and < 2.5%, respectively). It was applied to group identification and differentiation of different brands, models, and batches of red printing, stamp, and pen inks. It was demonstrated that differentiation can be performed effectively on the basis of migration times and ratios of peak areas. The high efficiency of the developed method was indicated by discriminating power ranging from 87.3 to 98.8%, for stamp and pen inks, respectively. The results showed that the proposed procedure can be valuable for an objective examination of the red parts of questioned documents.     

Direct sample introduction of wines in graphite furnace atomic absorption spectrometry for the simultaneous determination of arsenic, cadmium, copper and lead content

A multi-element graphite furnace atomic absorption spectrometry (GFAAS) method was elaborated for the simultaneous determination of As, Cd, Cu, and Pb in wine samples of various sugar contents using the transversally heated graphite atomizer (THGA) with end-capped tubes and integrated graphite platforms (IGPs). For comparative GFAAS analyses, direct injection (i.e., dispensing the sample onto the IGP) and digestion-based (i.e., adding oxidizing agents, such as HNO(3) and/or H(2)O(2) to the sample solutions) methods were optimized with the application of chemical modifiers. The mixture of 5 microg Pd (applied as nitrate) plus 3 microg Mg(NO(3))(2) chemical modifier was proven to be optimal for the present set of analytes and matrix, it allowing the optimal 600 degrees C pyrolysis and 2200 degrees C atomization temperatures, respectively. The IGP of the THGA was pre-heated at 70 degrees C to prevent the sputtering and/or foaming of sample solutions with a high organic content, dispensed together with the modifier solution, which method also improved the reproducibility of the determinations. With the digestion-based method, the recovery ranged between 87 and 122%, while with the direct injection method it was between 96 and 102% for Cd, Cu, and Pb, whereas a lower, compromise recovery of 45-85% was realized for As. The detection limits (LODs) were found to be 5.0, 0.03, 1.2, and 0.8 microg l(-1) for As, Cd, Cu, and Pb, respectively. The characteristic mass (m(0)) data were 24 pg As, 1.3 pg Cd, 13 pg Cu, and 35 pg Pb. The upper limits of the linear calibration range were 100, 2, 100, and 200 microg l(-1) for As, Cd, Cu, and Pb, respectively. The precisions were not worse than 4.8, 3.1, 3.7, and 2.3% for As, Cd, Cu, and Pb, respectively. For arsenic, a higher amount of the modifier (e.g., 20 microg Pd plus 12 microg Mg(NO(3))(2)) could be recommended to overcome the interference from the presence of sulphate and phosphate in wines. Although this method increased the sensitivity for As (m(0)=20 pg), it also enhanced the background noise, thus only a slight improvement in the LOD of As (3.9 microg l(-1)) was realized. For the 35 red and white wine samples studied, the highest metal contents were observed for Cu ranging from 20 to 640 microg l(-1) (average: 148 microg l(-1)), followed by Pb from 6 to 90 microg l(-1) (average: 32.3 microg l(-1)), and Cd from 0.05 to 16.5 microg l(-1) (average: 1.06 microg l(-1)), whereas the As content was below the LOD. This wide fluctuation in the trace metal content could be associated with the origin of wines from various regions (i.e., different trace metal level and/or quality of soil, and/or anthropogenic impact), and with diverse materials (e.g., additives and containers) involved in the wine production processes. The Cu content of wine samples was significantly correlated with Pb, whereas its weak anti-correlation was found with Cd. Interestingly, the level of Pb was anti-correlated with the year of production of the wines. This is likely due to the gradual decrease in the Pb content of soils of vineyards by time, which certainly causes less Pb-uptake of the grape plant, thus a decrease in the Pb content of wines as well.     

Rhodium(I)-catalyzed cycloisomerizations of bicyclobutanes

The selection of rhodium precatalyst and phosphine ligand determines the course of the cycloisomerization of N-allylated bicyclo[1.1.0]butylalkylamines. Cyclopropane-fused pyrrolidines and azepines are obtained with high levels of stereo- and regiocontrol. Novel azatricyclo[6.1.0.0(1,5)]nonanes are the result of a tandem cycloisomerization-ring closing metathesis sequence. Allylic ethers lead to furans and oxepanes.     

Discrimination of biofilm samples using pattern recognition techniques

Biofilms are complex aggregates formed by microorganisms such as bacteria, fungi and algae, which grow at the interfaces between water and natural or artificial materials. They are actively involved in processes of sorption and desorption of metal ions in water and reflect the environmental conditions in the recent past. Therefore, biofilms can be used as bioindicators of water quality. The goal of this study was to determine whether the biofilms, developed in different aquatic systems, could be successfully discriminated using data on their elemental compositions. Biofilms were grown on natural or polycarbonate materials in flowing water, standing water and seawater bodies. Using an unsupervised technique such as principal component analysis (PCA) and several supervised methods like classification and regression trees (CART), discriminant partial least squares regression (DPLS) and uninformative variable elimination–DPLS (UVE-DPLS), we could confirm the uniqueness of sea biofilms and make a distinction between flowing water and standing water biofilms. The CART, DPLS and UVE-DPLS discriminant models were validated with an independent test set selected either by the Kennard and Stone method or the duplex algorithm. The best model was obtained from CART with 100% correct classification rate for the test set designed by the Kennard and Stone algorithm. With CART, one variable describing the Mg content in the biofilm water phase was found to be important for the discrimination of flowing water and standing water biofilms.     

The structure of Fe(III) ions in strongly alkaline aqueous solutions from EXAFS and Mössbauer spectroscopy

To establish the structure of ferric ions in strongly alkaline (pH > 13) environments, aqueous NaOH solutions supersaturated with respect to Fe(III) and the solid ferric-hydroxo complex salts precipitating from them have been characterized with a variety of experimental techniques. From UV measurements, in solutions of pH > 13, only one kind of Fe(III)-hydroxo complex species was found to be present. The micro crystals obtained from such solutions were proven to be a new, so far unidentified solid phase. M?ssbauer spectra of the quick-frozen solution and that of the complex salt indicated a highly symmetrical ferric environment in both systems From the EXAFS and XANES spectra, the environment of the ferric ion in these solutions (both native and quick-frozen) and in the complex salt was found to be different. In the complex salt, the bond lengths are consistent with an octahedral coordination around the ferric centres. In solution, the coordination geometry of Fe(III) is most probably tetrahedral. Our results demonstrate that in strongly alkaline aqueous solutions, ferric ions behave very similarly to other structurally related tervalent ions, like Al(III) or Ga(III).     

Collapse of warped foliations

The aim of this note is to generalize the concept of warped product to a foliated manifold (M,F,g) as follows: If is a smooth function constant along the leaves of the foliation F then new metric structure gf on the manifold M is constructed as follows: gf(v,w)=f²g(v,w) if v,w are tangent to F and gf(v,w)=g(v,w) if v or w is perpendicular to F. A foliated manifold (M,F,gf) is called warped foliation while f is called warping function.Next, if is a sequence of warping functions on M, the question of the existence of the limit in Gromov-Hausdorff of a sequence ((M,F,gfn))_n∈N warped foliation is asked. A number of examples is considered such foliations with dense leaf or foliations consisting of finite number of Reeb components. Next, sufficient and necessary condition of converging in Gromov-Hausdorff sense of a Riemannian foliation with all leaves compact to the space of leaves with a metric defined by Hausdorff distance of leaves is developed. Finally some results on Hausdorff foliations with all leaves compact are shown.     

Computational Analysis of Ca2+ Oscillatory Bio-Signals: Two-Parameter Bifurcation Diagrams

Two types of bifurcation diagrams of cytosolic calcium nonlinear oscillatory systems are presented in rectangular areas determined by two slowly varying parameters. Verification of the periodic dynamics in the two-parameter areas requires solving the underlying model a few hundred thousand or a few million times, depending on the assumed resolution of the desired diagrams (color bifurcation figures). One type of diagram shows period-n oscillations, that is, periodic oscillations having n maximum values in one period. The second type of diagram shows frequency distributions in the rectangular areas. Each of those types of diagrams gives different information regarding the analyzed autonomous systems and they complement each other. In some parts of the considered rectangular areas, the analyzed systems may exhibit non-periodic steady-state solutions, i.e., constant (equilibrium points), oscillatory chaotic or unstable solutions. The identification process distinguishes the later types from the former one (periodic). Our bifurcation diagrams complement other possible two-parameter diagrams one may create for the same autonomous systems, for example, the diagrams of Lyapunov exponents, Ls diagrams for mixed-mode oscillations or the 0–1 test for chaos and sample entropy diagrams. Computing our two-parameter bifurcation diagrams in practice and determining the areas of periodicity is based on using an appropriate numerical solver of the underlying mathematical model (system of differential equations) with an adaptive (or constant) step-size of integration, using parallel computations. The case presented in this paper is illustrated by the diagrams for an autonomous dynamical model for cytosolic calcium oscillations, an interesting nonlinear model with three dynamical variables, sixteen parameters and various nonlinear terms of polynomial and rational types. The identified frequency of oscillations may increase or decrease a few hundred times within the assumed range of parameters, which is a rather unusual property. Such a dynamical model of cytosolic calcium oscillations, with mitochondria included, is an important model in which control of the basic functions of cells is achieved through the Ca2+ signal regulation.