Kinetic Analysis of the Reactions between GG-Containing Oligonucleotides and Platinum Complexes. 1. Reactions of Single-Stranded Oligonucleotides with cis-[Pt(NH(3))(2)(H(2)O)(2)](2+) and [Pt(NH(3))(3)(H(2)O)](2+)

Using concentration measurements based on high performance liquid chromatography, we have investigated the kinetics of reaction between single-stranded oligonucleotides containing a d(GpG) sequence, i.e., d(GG), d(TGG), d(TTGG), and d(CTGGCTCA), and the platinum complexes cis-[Pt(NH(3))(2)(H(2)O)(2)](2+) (1) and [Pt(NH(3))(3)(H(2)O)](2+) (2). The rate constants for the substitution of one aqua ligand of platinum in 1 or 2 by each guanine of the oligonucleotides were individually measured, as well as, for 1, those for the subsequent conversion of the monoadducts to the diadduct. For the platination of d(GG) and d(TGG), the rate constants are similar for the 5'- and 3'-guanines. The longer oligonucleotides d(TTGG) and d(CTGGCTCA) are platinated slightly faster on the 5'-G than on the 3'-G. 2 shows a similar slight preference for the 5'-guanine, but it reacts by a factor of 4-10 more slowly than 1. For both complexes, the platination rate constants increase with increasing oligonucleotide length. Platination of the 5'-G by 1 is 1 order of magnitude faster on d(CTGGCTCA) than on d(GG). Concerning the chelation step giving the GG diadduct of 1, the longer the oligonucleotide, the larger is the ratio between the rates of the cyclization of the 3'- and 5'-monoadducts k(3)(')(c) and k(5)(')(c): k(3)(')(c)/k(5)(')(c) equals 1.4 for d(GG) and 3.3 for d(CTGGCTCA).     

Exchange of deuterium with OH groups of HY zeolites

The exchange reaction of D₂ with OH groups of HY zeolites was followed both in the solid and gas phase by IR and MS. The rates of D₂–OH and D₂–H₂ exchange increase considerably with dehydroxylation of the sample. The active centers are probably vacancies formed by removal of oxygen from the lattice, they catalyze the dissociation of D₂. Dehydroxylation of the sample is accompanied by the formation of 3 740 cm^–1 hydroxyls, whose exchange with D₂ is slower than that with other OH groups and which affect the kinetics in the gas phase.

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D₂ OH HY - O₂–OH O₂–H₂ . , , , O₂. OH, 3740 ^–1, , OH .

     

Topographical properties of polymer films deposited in capillaries for electrophoretic separations of large organic molecules

Topography and thickness of hydrophilic polymer coatings of fused-silica capillaries for capillary electrophoresis (CE) were investigated using atomic force microscopy (AFM), scanning electron microscopy (SEM), and profilometry. Three hydrogels, poly(2-hydroxyethyl methacrylate) [poly(HEMA)], poly(diethylene glycol monomethacrylate) [poly(DEGMA)], and poly(triethylene glycol monomethacrylate) [poly(TEGMA)], were deposited using two procedures, either by simple physical sorption of the polymers, or by derivatization of the capillary wall surface with glycidyl methacrylate (EPMA) followed by polymerization of the appropriate monomers. The performance of the modified capillaries was tested under CE conditions (decrease in the electroosmotic flow, EOF dependence on pH, separation of milk and standard proteins). It has been found that the most important property of the polymer coating is its thickness, whereas its topography and the degree of its hydrophobicity are less significant. Film deposition by physical adsorption is preferable to polymerization on the derivatized surface.     

Regulation of the excitation energy utilization in the photosynthetic apparatus of chlorina f2 barley mutant grown under different irradiances

Acclimation of the photosynthetic apparatus of chlorophyll b-less barley mutant chlorina f2 to low light (100 micromolm(-2)s(-1); LL) and extremely high light level (1000 micromolm(-2)s(-1); HL) was examined using techniques of pigment analysis and chlorophyll a fluorescence measurements at room temperature and at 77 K. The absence of chlorophyll b in LL-grown chlorina f2 resulted in the reduction of functional antenna size of both photosystem II (by 67%) and photosystem I (by 21%). Chlorophyll fluorescence characteristics of the LL-grown mutant indicated no impairment of the utilization of absorbed light energy in photosystem II photochemistry. Thermal dissipation of excitation energy estimated as non-photochemical quenching of minimal fluorescence (SV(0)) was significantly higher as compared to the wild-type barley grown under LL. Despite impaired assembly of pigment-protein complexes, chlorina f2 was able to efficiently acclimate to HL. In comparison with chlorina f2 grown under LL, HL-grown chlorina f2 was characterized by unaffected maximal photochemical efficiency of photosystem II (F(V)/F(M), doubled content of both beta-carotene and the xanthophyll cycle pigments and considerably reduced efficiency of excitation energy transfer from carotenoids to chlorophyll a. The enormous xanthophyll cycle pool size was however associated with reduced SV(0) capacity. We suggest that the substantial part of the xanthophyll cycle pigments is not bound to the remaining pigment-protein complexes and acts as filter for excitation energy, thereby contributing to the efficient photoprotection of chlorina f2 grown under HL.     

Protection of the Hydroxyphosphinyl Function of Phosphinic Dipeptides by Adamantyl. Application to the Solid-Phase Synthesis of Phosphinic Peptides

To develop solid-phase synthesis of phosphinic peptides, different FmocXaaPsi{PO(OAd)CH(2)}XaaOH building blocks have been prepared, where Fmoc is (fluorenylmethoxy)carbonyl. In this respect, the protection of the hydroxyphosphinyl function in these phosphinic dipeptides by the adamantyl group turns out to be convenient. The phosphinic adamantyl esters are completely stable in basic conditions and can be removed under relatively mild acidic conditions. Using these building blocks, despite the bulkiness of the adamantyl group, no particular problem of coupling was observed during the solid-phase synthesis of phosphinic peptides by the Fmoc strategy. The developed methodology is of particular interest to facilitate the development of potent inhibitors of zinc-metalloproteases.     

Non-Watson-Crick base pairing in RNA. quantum chemical analysis of the cis Watson-Crick/sugar edge base pair family

Large RNA molecules exhibit an astonishing variability of base-pairing patterns, while many of the RNA base-pairing families have no counterparts in DNA. The cis Watson-Crick/sugar edge (cis WC/SE) RNA base pairing is investigated by ab initio quantum chemical calculations. A detailed structural and energetic characterization of all 13 crystallographically detected members of this family is provided by means of B3LYP/6-31G and RIMP2/aug-cc-pVDZ calculations. Further, a prediction is made for the remaining 3 cis WC/SE base pairs which are yet to be seen in the experiments. The interaction energy calculations point at the key role of the 2'-OH group in stabilizing the sugar-base contact and predict all 16 cis WC/SE base-pairing patterns to be nearly isoenergetic. The perfect correlation of the main geometrical parameters in the gas-phase optimized and X-ray structures shows that the principle of isosteric substitutions in RNA is rooted from the intrinsic structural similarity of the isolated base pairs. The present quantum chemical calculations for the first time analyze base pairs involving the ribose 2'-OH group and unambiguously correlate the structural information known from experiments with the energetics of interactions. The calculations further show that the relative importance and absolute value of the dispersion energy in the cis WC/SE base pairs are enhanced compared to the standard base pairs. This may by an important factor contributing to the strength of such interactions when RNA folds in its polar environment. The calculations further demonstrate that the Cornell et al. force field commonly used in molecular modeling and simulations provides satisfactory performance for this type of RNA interactions.     

Calcined Ni—Al layered double hydroxide as a catalyst for total oxidation of volatile organic compounds: Effect of precursor crystallinity

The effect of hydrothermal treatment on properties (crystallinity, porous structure, reducibility, acidity, basicity, and catalytic activity and selectivity in toluene and ethanol total oxidation) of Ni—Al layered double hydroxide precursors and related mixed oxides was examined. The hydrothermal treatment increased considerably both the content of crystalline phase and LDH crystallite size. On the other hand, only a slight effect of the precursor hydrothermal treatment on crystallinity of the related Ni—Al mixed oxides obtained by calcination at 450°C was observed. The reducibility of NiO particles appeared to be hindered considerably compared to the reducibility of pure NiO. Catalytic activity of the Ni—Al mixed oxides prepared from the precursors hydrothermally treated for a short time (4 h) was the highest. The highest amount of acetaldehyde formed during the total oxidation of ethanol, i.e. the worst selectivity was found for the calcined Ni—Al LDH without hydrothermal treatment. Presented at the 33rd International Conference of the Slovak Society of Chemical Engineering, Tatranské Matliare, 22–26 May 2006.     

Utilization of zirconia stationary phase as a tool in drug control

Zirconia-based stationary phases represent an interesting alternative to silica-based materials. Two zirconia-based stationary phases were studied as an option for use in drug analysis. The different properties of zirconia material, distinct from RP silica-columns, were employed for the development of a novel and rapid stability monitoring HPLC method. This method enables simultaneous control of possible degradation processes of active substance (ibuprofen) as well as antimicrobial excipients (methyl-and propylparaben). The separation of ibuprofen, its two main degradation products 2-(4-isobutyrylphenyl)propionic acid and 4-isobutylacetophenone, parabens, and 4-hydroxybenzoic acid as their degradation product was successfully accomplished on a Zr-CarbonC18 column using a mobile phase consisting of acetonitrile-phosphate buffer (pH 4.8)-propan-2-ol (27:56:17, v/v/v). Detection was performed at 258 nm and the analysis was completed within 17 minutes.     

Air/polymer distribution coefficients for polycyclic aromatic hydrocarbons by solid-phase microextraction sampling

Two methods to estimate distribution coefficients (K) between air and poly(dimethylsiloxane) (PDMS) coating of solid-phase microextraction (SPME) fibers for eight low molecular polycyclic aromatic hydrocarbons (PAHs) there are presented. The PDMS phases were used for determination of the coefficients according to equilibrium theory with help of a developed static calibration system (SCS). Another way to estimate the coefficients is based on the use of a linear relationship between the logarithm of the coefficients (log K) and linear temperature-programmed retention indexes (LTPRI) of the compounds without necessity to calibrate. The log K values for both of methods ranged from 5.2 (naphthalene) to 8.9 (pyrene) at 22 degrees C. Relative standard deviation (R.S.D.) of log K for each compound determined by static calibration was no more than 5.3%. R.S.D. of retention times for LTPRI indices did not exceed 0.28% for repeated injection. All experiments were implemented on a GC-MS system.     

Phase Equilibria in the Ni–Al–W System at 900°C

Multicomponent Ni-base alloys exhibit good mechanical properties even at elevated temperatures and they are widely used for industrial production of exertion-resistive parts of engines. These properties are mainly determined by the coexistence of a disordered γ matrix with a face centred cubic lattice and cuboidal domains of its ordered γ′ structure. Therefore it is useful to study phase equilibria in Ni-base systems, namely in the regions involving both mentioned phases. One of the conclusions of our recent work on Ni–Al–Cr–W system was a necessity of modification of selected thermodynamic parameters of the ternary Ni–Al–W subsystem in order to achieve a better agreement of our experimental observations with theoretical modelling. This involves new measurements of the microstructure of selected samples of the Ni–Al–W system at 900°C and the comparison of the results with existing literature data in order to confirm our conclusions on higher order system investigated before. It is a first step on the way to an assessment of the Ni–Al–W system, which has not been done before.