Segmentation of Heteropolymer Sequences Specifying Subsequences with Different Composition and Statistical Properties

We have studied the segmentation of two‐letter AB heterosequences composed of subsequences with different composition and distribution of A and B monomer units along the chain. Our approach is based on the segmentation function S(k) introduced in the present work and on the Jensen–Shannon divergence measure determined with respect to the probabilities of the lengths of uniform blocks of A and B monomer units. It is shown that the function S(k) is extremely sensitive to the sequence statistics. Even visual analysis of S(k) allows judgment on some features of sequence statistics. In particular, function S(k) is constant for random copolymers, it is an oscillating function for random block copolymers and shows monotonic growth up to some constant value for proteinlike copolymers. However, due to significant fluctuations observed for short sequences, the function S(k) can be effectively used only for segmentation of a heterosequence composed of very long subsequences. On the other hand, we find that the Jensen–Shannon divergence measure does not allow one to judge the type of statistics, but is extremely efficient for segmentation of a heterosequence. Therefore, the two introduced functions, being mutually complementary, provide an effective approach for recognizing and segmentation of heterosequences. As an example, the methods developed are applied for concatenating sequences of different proteins.

Segmentation function S(k, l, x) as a function of parameter k and starting number x of “window” for a sequence composed of elastin and ribonuclease sequences.     

The layered structure of poly­[[di‐μ‐chloro‐bis­[chloro(2‐ethyl­tetrazole‐κN4)copper(II)]]‐di‐μ‐2‐ethyl­tetrazole‐κ2N1:N4]

In the polymeric title complex, [CuCl₂(C₃H₆N₄)₂]_n, there are two ligands in the asymmetric unit. The Cu atom adopts an elongated octahedral geometry, with two 2‐ethyl­tetrazole ligands [Cu—N = 2.0037 (16) and 2.0136 (16) Å] and two Cl atoms [Cu—Cl = 2.2595 (6) and 2.2796 (6) Å] in equatorial positions. A Cl atom and a symmetry‐related 2‐ethyl­tetrazole mol­ecule [Cu—Cl = 2.8845 (8) Å and Cu—N = 2.851 (2) Å] lie in the axial positions of the octahedron. One of the two 2‐­ethyltetrazole ligands of the asymmetric unit exhibits bidentate binding to two Cu atoms through two N atoms of the tetrazole ring, whereas the other ligand is coordinated in a monodentate fashion via one tetrazole N atom. The Cu‐atom octahedra form dimer entities by sharing edges with equatorial and axial Cl atoms. The dimers are linked together through the 2‐ethyl­tetrazole ligands to form one‐dimensional polymeric zigzag chains extending along the b axis. The chains are connected into infinite layers parallel to the (10) plane via the 2‐ethyl­tetrazole ligands.     

High-throughput capillary electrophoretic method for determination of total aminothiols in plasma and urine.

Increased interest in the analysis of aminothiols in body fluids during the last years results in a request for high-throughput analytical methods for their determination. We report here a novel, high-throughput method for the determination of total concentrations of biogenous aminothiols - homocysteine, cysteine, glutathione, cysteinylglycine, gamma-glutamylcysteine, and of penicilamine, mercaptopropionylglycine, and cysteamine, three compounds used to treat disorders of aminothiol metabolism in plasma and urine. Samples were reduced with tris(carboxyethyl)phosphine and labeled with 5-(bromomethyl)fluorescein. Capillary electrophoretic separations were performed in 60 mmol/L borate - 15 mmol/L sodium dodecyl sulfate - 2-amino-2-methyl-1-propanol, pH 10.0, with laser-induced fluorescence detection. Analysis time was less than 2 min. The assay is linear (r > 0.999) up to 500 micromol/L. Reproducibilities of migration times (coefficient of variation, CV) were < 0.5%. Interassay repeatabilities (CV, n = 10) were 5.08% and 6.09% for 5 micromol/L addition of homocysteine and 0.60% and 3.78% for 100 micromol/L addition of cysteine in plasma and urine, respectively. Recovery values were within 94-106% and sensitivity was better than 0.19 micromol/L for all analyzed compounds. Results agreed well with a standard high-performance liquid chromatography (HPLC) method. The diagnostic usefulness of the method has been proven on 79 samples of cystinuric patients and 12 samples of homocystinuric patients. We report here a novel method for the determination of aminothiols in body fluids by capillary electrophoresis (CE). Determination is fast and sensitive enough for diagnostic purposes.     

Chiral separation of lansoprazole and rabeprazole by capillary electrophoresis using dual cyclodextrin systems

Novel capillary electrophoresis methods using CDs as chiral selectors were developed and validated for the chiral separation of lansoprazole and rabeprazole, two proton pump inhibitors. Fourteen different neutral and anionic CDs were screened at pH 4 and 7 in the preliminary analysis. Sulfobutyl‐ether‐β‐CD with a degree of substitution of 6.5 and 10 at neutral pH proved to be the most suitable chiral selector for both compounds. Various dual CD systems were also compared, and the possible mechanisms of enantiomer separation were investigated. A dual selector system containing sulfobutyl‐ether‐β‐CD degree of substitution 6.5 and native γ‐CD proved to be the most adequate system for the separations. Method optimization was carried out using an experimental design approach, performing an initial fractional factorial screening design, followed by a central composite design to establish the optimal analytical conditions. The optimized methods (25 mM phosphate buffer, pH 7, 10 mM sulfobutyl‐ether‐β‐CD/20 mM γ‐CD, +20 kV voltage; 17°C temperature; 50 mbar/3 s injection, detection at 210 nm for lansoprazole; 25 mM phosphate buffer, pH 7, 15 mM sulfobutyl‐ether‐β‐CD/30 mM γ‐CD, +20 kV voltage; 18°C temperature; 50 mbar/3 s injection, detection at 210 nm for rabeprazole) provided baseline separation for lansoprazole (R_s = 2.91) and rabeprazole (R_s = 2.53) enantiomers with favorable migration order (in both cases the S‐enantiomers migrates first). The optimized methods were validated according to current guidelines and proved to be reliable, linear, precise, and accurate for the determination of 0.15% distomer as chiral impurity in dexlansoprazole and dexrabeprazole samples.     

Thermal and electrical properties of Ca5Mg4−xZnx(VO4)6 (0 ≤ x ≤ 4)

Calcium vanadates Ca₅Mg_4−xZn_x(VO₄)₆ (0 ≤ x ≤ 4) have been studied for the first time using a set of high-temperature methods of analysis. The onset of melting process determined from differential scanning calorimetry decreases from 1158 to 881 °C (± 1.5 °C) with increasing of x (dopant’s content). CTE temperature dependence is found to show a hysteresis. Electrical transport properties measured by impedance spectroscopy in air of different humidity are also discussed. The value of electrical conductivity does not depend on air humidity. It is found to equal to 1.5 × 10⁻⁶ S cm⁻¹ at 720 °C for Ca₅Mg₄(VO₄)₆ which is specific for garnet-related crystals.

     

Excited-state dynamics of fac-[ReI(L)(CO)3(phen)]+ and fac-[ReI(L)(CO)3(5-NO2-phen)]+ (L = imidazole, 4-ethylpyridine; phen = 1,10-phenanthroline) complexes

The nature and dynamics of the lowest excited states of fac-[Re(I)(L)(CO)(3)(phen)](+) and fac-[Re(I)(L)(CO)(3)(5-NO(2)-phen)](+) [L = Cl(-), 4-ethyl-pyridine (4-Etpy), imidazole (imH); phen = 1,10-phenanthroline] have been investigated by picosecond visible and IR transient absorption spectroscopy in aqueous (L = imH), acetonitrile (L = 4-Etpy, imH), and MeOH (L = imH) solutions. The phen complexes have long-lived Re(I) --> phen (3)MLCT excited states, characterized by CO stretching frequencies that are upshifted relative to their ground-state values and by widely split IR bands due to the out-of-phase A'(2) and A"nu(CO) vibrations. The lowest excited states of the 5-NO(2)-phen complexes also have (3)MLCT character; the larger upward nu(CO) shifts accord with much more extensive charge transfer from the Re(I)(CO)(3) unit to 5-NO(2)-phen in these states. Transient visible absorption spectra indicate that the excited electron is delocalized over the 5-NO(2)-phen ligand, which acquires radical anionic character. Similarly, involvement of the -NO(2) group in the Franck-Condon MLCT transition is manifested by the presence of an enhanced nu(NO(2)) band in the preresonance Raman spectrum of [Re(I)(4-Etpy)(CO)(3)(5-NO(2)-phen)](+). The Re(I) --> 5-NO(2)-phen (3)MLCT excited states are very short-lived: 7.6, 170, and 43 ps for L = Cl(-), 4-Etpy, and imH, respectively, in CH(3)CN solutions. The (3)MLCT excited state of [Re(I)(imH)(CO)(3)(5-NO(2)-phen)](+) is even shorter-lived in MeOH (15 ps) and H(2)O (1.3 ps). In addition to (3)MLCT, excitation of [Re(I)(imH)(CO)(3)(5-NO(2)-phen)](+) populates a (3)LLCT (imH --> 5-NO(2)-phen) excited state. Most of the (3)LLCT population decays to the ground state (time constants of 19 (H(2)O), 50 (MeOH), and 72 ps (CH(3)CN)); in a small fraction, however, deprotonation of the imH.+ ligand occurs, producing a long-lived species, [Re(I)(im.)(CO)(3)(5-NO(2)-phen).-]+.     

Stationary-phase effects in gradient high-performance liquid chromatography

The type of the stationary phase for reversed-phase liquid chromatography significantly affects the sample polarity range that can be covered using gradients of organic solvents in water. The polarity range available for gradient separations of samples containing compounds differing in the lipophilic parts of the molecules can be characterized by "gradient lipophilic capacity", Pl, based on the retention of standard compounds with a repeat lipophilic structural unit, such as a methylene group. The gradient lipophilic capacity is also suitable to characterize the separation possibilities of the columns in non-aqueous reversed-phase gradient elution of strongly non-polar compounds, such as triacylglycerols. In the same way, the suitability of various columns for reversed-phase gradient separations of oligomers can be characterized by "gradient oligomer capacity", as demonstrated in the example of oligo(ethylene glycols). To enable a comparison of the properties of stationary phases independent of column efficiency and dimensions, the gradient lipophilic capacity or the gradient oligomer capacity should be normalized for a "standard" column plate number, gradient range and volume (in column hold-up volume units). The gradient lipophilic capacity or the gradient oligomer capacity and the number of compounds that can be resolved during a gradient run decrease as the initial concentration of the strong solvent in the mobile phase increases and (or) the gradient time decreases. These quantities can be used to select a suitable column and to adjust the optimum gradient profile (the initial composition of the mobile phase and the gradient steepness) with respect to the time of analysis and the number of oligomers or other compounds with regular repeat structural groups that can be resolved during the gradient run.     

Novel radial oligothienyl silanes

A series of thiophene-based homologues with a silicon core surrounded by mono-, bi-, terthiophene, and their derivatives with alkylsilyl linkages has been prepared using hydrosilylation and Stille coupling methods.     

Structure of Aqueous Gallium(III) Bromide Solutions Over a Temperature Range 80–333 K by Raman Spectroscopy, X-ray Absorption Fine Structure, and X-ray Diffraction

The structure and complex formation of concentrated aqueous gallium(III) bromide (GaBr₃) solutions have been investigated over a temperature range 80–333 K by Raman spectroscopy, X-ray absorption fine structure (XAFS), and X-ray diffraction. The Raman spectra obtained at various [Br^?]/[Ga³⁺] molar ratios and temperatures have shown that complex formation between Ga³⁺ and Br^? occurs as a predominant species, with [GaBr₄]^? at [Ga³⁺] as high as 1～2 M (M = mol?dm ^?3) and [Br^?]/[Ga³⁺] ratios > ～2, and that cooling of the solutions favors the formation of the aqua Ga³⁺. The intermediate species were not seen in the Raman spectra. The XAFS data have revealed that the aqua complex has a sixfold coordination as [Ga(H₂O)₆]³⁺ with a Ga³⁺–H₂O distance of (1.96 ± 0.02) Å, whereas the [GaBr₄]^? complex has a Ga³⁺–Br^? distance of (2.33± 0.02) Å, and that vitrification of the aqueous GaBr₃ solution at liquid nitrogen temperature shifts the equilibrium toward the aqua complex. The X-ray diffraction data at different subzero temperatures have shown a tendency of decreasing Ga³⁺–Br^? and increasing Ga³⁺–H₂O interactions with lowering temperature, confirming the preference of aqua Ga³⁺ in the supercooled liquid state as well as in the glassy state. The Ga³⁺–H₂O distance of ～1.8 Å for the tetrahedral coordination was found in a 2.01 M gallium(III) bromide solution with a [Br^?]/[Ga³⁺] ratio of 3.7 and gradually increased to a value of 1.92 Å for octahedral geometry with decreasing temperature, suggesting that equilibrium shifts from [GaBr₄]^? to [Ga(H₂O)₆]³⁺ through intermediate species, [GaBr _n ]^(3?n)+ (n = 2 and 3). The Ga³⁺–Br^? and Br^?–Br^? distances within [GaBr₄]^? with an almost tetrahedral symmetry are (2.35± 0.02) and (3.82± 0.03) Å, respectively. The Ga³⁺ has the second hydration shell at (4.03± 0.03) Å and the hydration of Br^? is characterized with a Br^?–H₂O distance of (3.35± 0.02) Å at all temperatures investigated.     

Fluorescence properties of some 2-(4-amino-substituted-3-nitrophenyl)-3-hydroxyquinolin-4(1H)-ones

2-(4-Amino-substituted-3-nitrophenyl)-3-hydroxyquinolin-4(1H)-ones have been studied to evaluate their fluorescence properties and possible use as molecular fluorescent probes. The amino group was substituted with various alkyl moieties possessing a suitable terminal functional group (such as hydroxy or amino group) that could serve to bind a 3-hydroxyquinolin-4(1H)-one (3HQ) fluorescence label to a biomolecule. Besides simple hydrocarbon chains, ligands containing ethylenoxy units as optimal spacers were also tested. The structure-fluorescence properties and theoretical applicability of the studied molecules are discussed.