Two-metal-ion mechanism for hammerhead-ribozyme catalysis

The hammerhead ribozyme is one of the best studied ribozymes, but it still presents challenges for our understanding of RNA catalysis. It catalyzes a transesterification reaction that converts a 5',3' diester to a 2',3' cyclic phosphate diester via an S(N)2 mechanism. Thus, the overall reaction corresponds to that catalyzed by bovine pancreatic ribonuclease. However, an essential distinguishing aspect is that metal ions are not involved in RNase catalysis but appear to be important in ribozymes. Although various techniques have been used to assign specific functions to metals in the hammerhead ribozyme, their number and roles in catalysis is not clear. Two recent theoretical studies on RNA catalysis examined the reaction mechanism of a single-metal-ion model. A two-metal-ion model, which is supported by experiment and based on ab initio and density functional theory calculations, is described here. The proposed mechanism of the reaction has four chemical steps with three intermediates and four transition states along the reaction pathway. Reaction profiles are calculated in the gas phase and in solution. The early steps of the reaction are found to be fast (with low activation barriers), and the last step, corresponding to the departure of the leaving group, is rate limiting. This two-metal-ion model differs from the models proposed previously in that the two metal ions function not only as Lewis acids but also as general acids/bases. Comparison with experiment shows good agreement with thermodynamic and kinetic data. A detailed analysis based on natural bond orbitals (NBOs) and natural energy decomposition (NEDA) provides insights into the role of metal ions and other factors important for catalysis.     

Feasibility of 1-Tbit/s (25 x 40 Gbit/s) transoceanic optically regenerated systems

The feasibility of 1-Tbit/s transoceanic systems based on in-line optical regeneration of 40-Gbit/s channels is numerically investigated. The roles of fiber dispersion, fiber mode area, and channel and regenerator spacings are analyzed, and the corresponding operating ranges for error-free transmission are determined. The results represent a first step in designing multi-terabit-per-second global transmission systems based on realistic components and parameters.     

Excited states of gaseous ions. IV. Potential energy surfaces of the H2O+ ion

Cross-sections of the potential energy hypersurfaces are reported for the four lower-lying states of the H₂O⁺ molecular ion. The symmetric dissociation of the ion has been investigated using the CNDO/2 method supplemented by a configuration interaction calculation. Self-consistent-field wave functions were calculated for the asymmetric dissociation using an extended basis of Gaussian-lobe functions. The values of the hydrogen exponents are found to be very sensitive to the molecular geometry. The calculated equilibrium H-O-H angle is 123° in the X?²B₁ state, nearly 180° in the X?A²A₁ state and 69° in the B?²B₂ state. The lower-lying quartet á ⁴B₁ is line entirely repulsive. The potential energy surface of the à ²A₁ state has a peculiar shape, characterized by two dissociation valleys.     

A first principles calculations and experimental study of the ground- and excited-state properties of ladder oligo(p-aniline)s

The molecular structure of three ladder oligo(p-aniline)s, 5,11-diethyl-6,12-dimethylindolo[3,2-b]carbazole (DIMER 2P), 14-ethyl-5,8-dihydro-diindolo[3,2-b:2',3'-h]carbazole (TRIMER 2P), and 5,8,14-triethyl-diindolo[3,2-b:2',3'-h]carbazole (TRIMER 3P) were investigated by first principles calculations at the Hartree-Fock (HF6-31G*) and density functional theory (DFTB3LYP6-31G*) levels. It is found that the agreement between theoretical and x-ray geometrical parameters is good and rather similar for both theoretical methods. The nature and the energy of the first two singlet-singlet electronic transitions have been obtained by Zerner intermediate neglect of differential overlap/spectroscopy semiempirical calculations performed on the HF6-31G* and DFTB3LYP6-31G* optimized geometries, as well as time-dependent density functional theory (TDDFT) calculations performed on the DFTB3LYP6-31G* optimized structures. For all the compounds and for all the theoretical approaches, it is observed that the S(1)<--S(0) electronic transition (pipi*) is weakly allowed and polarized along the short axis (y) of the molecule. On the other hand, the S(2)<--S(0) electronic transition of each oligomer possesses a much larger oscillator strength and is polarized along the long (x) molecular axis. It is found that TDDFT calculations provide the best overall agreement between the energies and the corresponding optical transitions obtained from the absorption bands (0-0 peaks) measured in dichloromethane as well as providing a good evaluation of the bathochromic shifts caused by the increase in the conjugation length or by the presence of extra alkyl chains on the nitrogen atoms in TRIMER 3P compared to TRIMER 2P.     

Isolation of 6-mercaptopurine in human plasma by aluminum ion complexation for high-performance liquid chromatographic analysis

A sample preparation technique and a high-performance liquid chromatographic method for 6-mercaptopurine (6-MP) that is simple, sensitive and without interference from its metabolites is described. 6-Thioguanine (6-TG) is added as an internal standard to the plasma sample, which is then treated with an aqueous solution of aluminum perchlorate to denature the plasma proteins and form complexes with 6-TG, 6-MP and its major metabolite, 6-thiouric acid (6-TUA). These complexes coprecipitate with proteins on centrifugation. 6-MP and its analogues are then extracted from the precipitate with perchloric acid containing sodium hydrosulfite and the extract is chromatographed on an Ultrasphere ODS column eluted with 0.1 M phosphoric acid and 0.001 M dithiothreitol in deionized water. The eluate is monitored at 340 nm. No interfering peak was encountered in over 300 clinical plasma samples. 6-TUA was separated from 6-MP and was found to be present in much higher concentration than 6-MP itself throughout the sampling time (6 h) following oral administration of the drug.     

The palladium(II)-catalyzed Nazarov reaction

The PdCl(2)-catalyzed cyclization of alpha-alkoxy dienones leads to 2-hydroxycyclopentenones, whereas the Pd(OAc)(2)-catalyzed reaction leads to cross-conjugated cyclopentenones through an oxidative process. [reaction: see text]     

Experimental and modeling study of the oxidation of xylenes

This paper describes an experimental and modeling study of the oxidation of the three isomers of xylene (ortho‐, meta‐, and para‐xylenes). For each compound, ignition delay times of hydrocarbon–oxygen–argon mixtures with fuel equivalence ratios from 0.5 to 2 were measured behind reflected shock waves for temperatures from 1330 to 1800 K and pressures from 6.7 to 9 bar. The results show a similar reactivity for the three isomers. A detailed kinetic mechanism has been proposed, which reproduces our experimental results, as well as some literature data obtained in a plug flow reactor at 1155 K showing a clear difference of reactivity between the three isomers of xylene. The main reaction paths have been determined by sensitivity and flux analyses and have allowed the differences of reactivity to be explained. © 2006 Wiley Periodicals, Inc. Int J Chem Kinet 38: 284–302, 2006     

Ueber die Bestimmung der St?rke in Cerealien, Kartoffeln und in der Handelsst?rke

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