Design, synthesis, and evaluation of a biomimetic artificial photolyase model

Two new artificial photolyase models that recognize pyrimidine dimers in protic and aprotic organic solvents as well as in water through a combination of charge and hydrogen-bonding interactions and use a mimic of the flavine to achieve repair through reductive photoinduced electron transfer are presented. Fluorescence and NMR titration studies show that it forms a 1:1 complex with pyrimidine dimers with binding constants of approximately 10(3) M(-1) in acetonitrile or methanol, while binding constants in water at pH 7.2 are slightly lower. Excitation of the complex with visible light leads to clean and rapid cycloreversion of the pyrimidine dimer through photoinduced electron transfer catalysis. The reaction in water is significantly faster than in organic solvents. The reaction slows down at higher conversions due to product inhibition.     

Quantitative analysis of backbone dynamics in a crystalline protein from nitrogen-15 spin-lattice relaxation

A detailed analysis of nitrogen-15 longitudinal relaxation times in microcrystalline proteins is presented. A theoretical model to quantitatively interpret relaxation times is developed in terms of motional amplitude and characteristic time scale. Different averaging schemes are examined in order to propose an analysis of relaxation curves that takes into account the specificity of MAS experiments. In particular, it is shown that magic angle spinning averages the relaxation rate experienced by a single spin over one rotor period, resulting in individual relaxation curves that are dependent on the orientation of their corresponding carousel with respect to the rotor axis. Powder averaging thus leads to a nonexponential behavior in the observed decay curves. We extract dynamic information from experimental decay curves, using a diffusion in a cone model. We apply this study to the analysis of spin-lattice relaxation rates of the microcrystalline protein Crh at two different fields and determine differential dynamic parameters for several residues in the protein.     

Cross-linking of polyolefins: a study by thermoporosimetry with benzene derivatives as swelling solvents.

The solvents o-, m-, p-xylene, p-dichlorobenzene, 1,2,4-trichlorobenzene, and naphthalene were calibrated as condensates used in the thermoporosimetry technique. Exponential relationships were found connecting the pore radii R(p) (in nm) and the freezing-point depression of the swelling solvent deltaT (in degrees C) on the one hand and the apparent energy of crystallization W(a) (in J cm(-3)) and deltaT on the other hand: R(p) = t exp[-1/(c deltaT)]; W(a) = W0 exp(deltaT/f). Pore- or mesh-size distributions can be derived from differential scanning calorimetry results by using the following equation: dV(p)/dR(p) = k{[cY(T)deltaT2]/[W(a)R(p)]}. All the numerical parameters were determined. Polyethylene and polypropylene samples, cross-linked with high-energy electrons or gamma-rays, were submitted to thermoporosimetry study. Relative mesh-size distributions, which depend on the polymer/solvent pair, were calculated for these polyolefins with o-, m-, and p-xylene as solvent and were found to be in the same sequence as those of their degrees of swelling and the irradiation doses received.     

Sensitive determination of josamycin and rokitamycin in plasma by high-performance liquid chromatography with fluorescence detection.

Rokitamycin and josamycin were successfully derivatized with dansylhydrazine in 20 min at 60 degrees C. Rokitamycin and josamycin levels were determined in plasma after ion-pair extraction into hexane-isoamyl alcohol with lauryl sulphate and precolumn derivatization. Resolution was obtained by liquid chromatography with fluorescence detection (352/537 nm) in 12 min. The limit of detection was 20 ng/ml macrolide starting from 1 ml of plasma, and linearity was demonstrated between 50 and 400 ng/ml. Inter-run coefficients of variation were 10.2% at 100 ng/ml and 9.1% at 300 ng/ml. The system was reliably used for pharmacokinetic studies in plasma.     

Surface organometallic chemistry of main group elements: selective synthesis of silica supported [triple bond Si-OB(C(6)F(5))(3)](-)[HNEt(2)Ph](+)

The reaction of the Lewis acid B(C(6)F(5))(3) with silanol groups of silica surfaces, dehydroxylated at different temperatures (300, 500, 700, and 800 degrees C), has been investigated in presence of the Br?nsted base NEt(2)Ph. The structure of the resulting modified silica supports [triple bond Si-OB(C(6)F(5))(3)](-)[HNEt(2)Ph](+) (1) has been carefully identified by IR and multinuclear solid-state NMR spectroscopies, isotopic (2)H and (18)O labeling, elemental analysis, molecular modeling, and comparison with synthesized molecular models. Highly dehydroxylated silica surfaces were required to transform selectively each silanol group into unique [triple bond Si-OB(C(6)F(5))(3)](-)[HNEt(2)Ph](+) fragments. For lower dehydroxylation temperatures, two sorts of surface sites were coexisting on silica: the free silanol groups [triple bond SiOH] and the ionic species 1.     

Electron capture dissociation of polypeptides using a 3 Tesla Fourier transform ion cyclotron resonance mass spectrometer

Electron capture dissociation (ECD) of polypeptides has been demonstrated using a commercially available 3 Tesla Fourier transform ion cyclotron resonance (FTICR) instrument. A conventional rhenium filament, designed for high-energy electron impact ionisation, was used to effect ECD of substance P, bee venom melittin and bovine insulin, oxidised B chain. A retarding field analysis of the effective electron kinetic energy distribution entering the ICR cell suggests that one of the most important parameters governing ECD for this particular instrument is the need to employ low trapping plate voltages. This is shown to maximise the abundance of low-energy electrons. The demonstration of ECD at this relatively low magnetic field strength could offer the prospect of more routine ECD analysis for the wider research community, given the reduced cost of such magnets and (at least theoretically) the greater ease of electron/ion cloud overlap at lower field.     

Efficient and fast Heck vinylation of 2-bromo-6-methyl pyridines with methylacrylate. Application to the synthesis of 6-methyl cyclopenta[b]pyridinone

Heck vinylation of 2-bromo-6-methyl-3-substituted pyridines using η³-allylpalladium chloride dimer/P(o-Tol)₃ complex/toluene and dimethylacetamide (DMA) as co-solvent with methyl acrylate is reported. Electronic and steric effects were investigated engaging diversely 2-bromo-3,6-disubstituted pyridines. As application, a new synthesis of the 6-methyl cyclopenta[b]pyridinone building-block connecting Heck vinylation, alkene reduction and Dieckmann condensation is described.     

Intramolecular C-glycosylation of 2-O-benzylated pentenyl mannopyranosides: remarkable 1,2-trans stereoselectivity

The IDCP-promoted intramolecular C-glycosylation of pentenyl α-mannopyranosides carrying, at O-2, an activated benzyl group gave, unexpectedly, the 1,2-trans-fused bicyclic product which corresponds to an α-C-aryl mannopyranose derivative. This remarkable, strained C-glycosyl compound was rapidly epimerized to the more stable 1,2-cis product on treatment with BF₃·Et₂O. The IDCP-reaction product could be elaborated into a 2-(α-C-mannopyranosyl)-3,4,5-trimethoxybenzyl alcohol derivative.     

Effects of DNA secondary structure on oligonucleotide probe binding efficiency

Secondary structure motifs in nucleic acid probes generally impair intended hybridization reactions and so efforts to predict and avoid such structures are commonly employed in probe design schemes. Another key facet of probe design that has received much less attention, however, is that secondary structure at targeted probe binding site regions may also impair hybridization. Thus, evaluation of both probe and target site secondary structures together should improve hybridization prediction and design effectiveness. Several challenges confound this goal, including imperfect empirical rules and parameters underlying predictions and the fact that folding algorithms scale poorly with respect to sequence length. Here, we attempt to quantify the consequences of target site structure on predicted hybridization using sequences sampled from the human genome. We also provide a methodology for choosing a reasonable “window size” around target sites that is as small as possible without compromising folding algorithm prediction accuracy.     

Reactivity of monolayer-protected gold nanoclusters at dye-sensitized liquid/liquid interfaces

Hexanethiolate monolayer-protected gold nanoclusters (MPCs) were used as redox quenchers at the polarizable water/1,2-dichloroethane (DCE) interface. Photocurrent responses originating from the heterogeneous quenching of photoexcited water soluble porphyrin complexes by MPCs dissolved in the DCE phase were observed. As MPCs can function as both electron acceptors and donors, the photocurrent results from the superposition of two simultaneous processes, which correspond to the oxidation and reduction of MPCs. The magnitude of the net photocurrent is essentially determined by the balance of the kinetics of these two processes, which can be controlled by tuning the Galvani potential difference between the two phases. We show that, within the available potential window, the apparent electron-transfer rate constants follow classical Butler-Volmer dependence on the applied potential difference.