Ab initio analytical potential energy surface and quasiclassical trajectory study of the O(+)((4)S)+H(2)(X (1)Sigma(g) (+))-->OH(+)(X (3)Sigma(-))+H((2)S) reaction and isotopic variants

An analytical potential energy surface (PES) representation of the O(+)((4)S)+H(2)(X (1)Sigma(g) (+)) system was developed by fitting around 600 CCSD(T)/cc-pVQZ ab initio points. Rate constant calculations for this reaction and its isotopic variants (D(2) and HD) were performed using the quasiclassical trajectory (QCT) method, obtaining a good agreement with experimental data. Calculations conducted to determine the cross section of the title reaction, considering collision energies (E(T)) below 0.3 eV, also led to good accord with experiments. This PES appears to be suitable for kinetics and dynamics studies. Moreover, the QCT results show that, although the hypotheses of a widely used capture model are not satisfied, the resulting expression for the cross section can be applied within a suitable E(T) interval, due to errors cancellation. This could be a general situation regarding the application of this simple model to ion-molecule processes.     

1,3-Dichloro-2-butene: a useful precursor for the 2-butene-1,3-dianion and its corresponding 1,3-dipolar synthon

The reaction of 1,3-dicloro-2-butene (1; 5:1 Z:E-mixture) with lithium powder and a catalytic amount of 4,4′-di-tert-butylbiphenyl (DTBB, 1% molar) in the presence of different electrophiles [EtCHO, PrⁱCHO, Bu^tCHO, c-C₆H₁₁CHO, Me₂CO, Et₂CO, (CH₂)₄CO, (CH₂)₅CO, (c-C₃H₅)₂CO, Me₃SiCl] in THF at temperatures ranging between −78 and −50°C gives, after hydrolysis with water, the corresponding products 2 in different Z:E-ratios depending on the electrophile used. Treatment of some diols 2 with hydrochloric acid gives dienic alcohols 3 or substituted dihydropyrans 4, depending on the structure of the starting diol. Finally, the same dichlorinated starting material is transformed into the corresponding allylic amines derived from morpholine and benzyl methyl amine and submitted to the same DTBB-catalysed lithiation as above, so after reaction with different electrophiles [Bu^tCHO, c-C₆H₁₁CHO, Me₂CO, Et₂CO, (CH₂)₄CO, (CH₂)₅CO, Me₃SiCl] and final hydrolysis with water, compounds 7 are isolated having a Z-configuration. A mechanistic explanation for this behaviour is given.     

Theoretical and photoluminescence studies on the d10-s2 AuI-TlI interaction in extended unsupported chains

The reactions of solutions of TlPF(6) and OPPh(3) in tetrahydrofuran or acetone with NBu(4)[AuR(2)] (R=C(6)Cl(5), C(6)F(5)) gave the new complexes [Au(C(6)Cl(5))(2)](2)[Tl(OPPh(3))][Tl(OPPh(3))(L)] (L=THF (1), acetone (2)) and the previously reported [Tl(OPPh(3))(2)][Au(C(6)F(5))(2)] (3). The crystal structures of complexes 1 and 2 display extended unsupported chains with short intermolecular interactions between alternating gold(I) and thallium(I) centres. Moreover, the Tl(I) centres show two different types of geometrical environments, such as pseudotetrahedral and distorted trigonal-bipyramidal, due to the presence of solvent molecules that act as ligands in the solid-state structure. Quasirelativistic and nonrelativistic ab initio calculations were performed to study the nature of the intermetallic Au(I)-Tl(I) interactions and are consistent with the presence of a high ionic contribution (80 %) and dispersion-type (van der Waals) interaction with a charge-transfer contribution (20 %) when relativistic effects are taken into account. All complexes are luminescent in the solid state at room temperature and at 77 K. Complexes 1 and 2 show site-selective excitation, probably due to the different environments around the Tl(I) centres. The DFT and time-dependent (TD)-DFT calculations are in agreement with the experimental excitation spectra for all complexes and confirm the site-selective excitation behaviour as a function of the Tl(I) geometrical environment.     

Mineral content and botanical origin of Spanish honeys

Eleven elements (Zn, P, B, Mn, Mg, Cu, Ca, Ba, Sr, Na and K) were determined by inductively plasma coupled spectrometry in 40 honey samples from different places of Spain and four different botanical origins: Eucalyptus (Eucalyptus sp.), Heather (Erica sp.), Orange-blossom (Citrus sinensis) and Rosemary (Rosmarinus officinalis). K, Ca and P show the higher levels with average concentrations ranged between 434.1-1935 mg kg⁻¹ for K; 42.59-341.0 mg kg⁻¹ for Ca and 51.17-154.3 mg kg⁻¹ for P. Levels of Cu (0.531-2.117 mg kg⁻¹), Ba (0.106-1.264 mg kg⁻¹) and Sr (0.257-1.462 mg kg⁻¹) are the lowest in all honey samples. Zn (1.332-7.825 mg kg⁻¹), Mn (0.133-9.471 mg kg⁻¹), Mg (13.26-74.38 mg kg⁻¹) and Na (11.69-218.5 mg kg⁻¹) concentrations were found strongly dependent on the kind of botanical origin.Results were submitted to pattern recognition procedures, unsupervised methods such as cluster and principal components analysis and supervised learning methods like linear discriminant analysis in order to evaluate the existence of data patterns and the possibility of differentiation of Spanish honeys from different botanical origins according to their mineral content. Cluster analysis shows four clusters corresponding to the four botanical origins of honey and PCA explained 71% of the variance with the first two PC variables. The best-grouped honeys were those from heather; eucalyptus honeys formed a more dispersed group and finally orange-blossom and rosemary honeys formed a less distinguishable group.     

Cross sections of the O+ + H2 --> OH+ + H ion-molecule reaction and isotopic variants (D2, HD): quasiclassical trajectory study and comparison with experiments

A dynamics study [cross section and microscopic mechanism versus collision energy (E(T))] of the reaction O+ + H2 --> OH+ + H, which plays an important role in Earth's ionosphere and interstellar chemistry, was conducted using the quasiclassical trajectory method, employing an analytical potential energy surface (PES) recently derived by our group [R. Martinez et al., J. Chem. Phys. 120, 4705 (2004)]. Experimental excitation functions for the title reaction, as well as its isotopic variants with D2 and HD, were near-quantitatively reproduced in the calculations in the very broad collision energy range explored (E(T) = 0.01-6.0 eV). Intramolecular and intermolecular isotopic effects were also examined, yielding data in good agreement with experimental results. The reaction occurs via two microscopic mechanisms (direct and nondirect abstraction). The results were satisfactorily interpreted based on the reaction probability and the maximum impact parameter dependences with E(T), and considering the influence of the collinear [OHH]+ absolute minimum of the PES on the evolution from reactants to products. The agreement between theory and experiment suggests that the reaction mainly occurs through the lowest energy PES and nonadiabatic processes are not very important in the wide collision energy range analyzed. Hence, the PES used to describe this reaction is suitable for both kinetics and dynamics studies.     

Hybrid Molecular Materials Based upon Organic π-Electron Donors and Inorganic Metal Complexes. Conducting Salts of Bis(ethylenediseleno)tetrathiafulvalene (BEST) with the Octahedral Anions Hexacyanoferrate(III) and Nitroprusside

The synthesis, structure and physical characterization of three new radical salts formed by the organic donor bis(ethylenediseleno)tetrathiafulvalene (BEDS-TTF or BEST) and the paramagnetic hexacyanoferrate(III) anion [Fe(CN)₆]³⁻ or the photochromic nitroprusside anion [Fe(CN)₅NO]²⁻ are reported: (BEST)₄[Fe(CN)₆] (1), (BEST)₃[Fe(CN)₆]₂·H₂O (2) and (BEST)₂[Fe(CN)₅NO] (3). Salts 1 and 3 show a layered structure with alternating organic (β-type packing) and inorganic slabs. Salt 2 shows an original interpenetrated structure probably due to the unprecedented presence of (BEST)²⁺ dications. The three salts are semiconductors although salt 1 exhibits a high room temperature conductivity and a semiconducting-semiconducting transition at ca. 150 K which has been attributed to a dimerization in the organic sublattice.     

Ethanol production from steam-explosion pretreated wheat straw

Bioconversion of cereal straw to bioethanol is becoming an attractive alternative to conventional fuel ethanol production from grains. In this work, the best operational conditions for steam-explosion pretreatment of wheat straw for ethanol production by a simultaneous saccharification and fermentation process were studied, using diluted acid [H₂SO₄ 0.9% (w/w)] and water as preimpregnation agents. Acid-or water-impregnated biomass was steam-exploded at different temperatures (160–200°C) and residence times (5, 10, and 20 min). Composition of solid and filtrate obtained after pretreatment, enzymatic digestibility and ethanol production of pretreated wheat straw at different experimental conditions was analyzed. The best pretreatment conditions to obtain high conversion yield to ethanol (approx 80% of theoretical) of cellulose-rich residue after steam-explosion were 190°C and 10 min or 200°C and 5 min, in acid-impregnated straw. However, 180°C for 10 min in acid-impregnated biomass provided the highest ethanol yield referred to raw material (140 L/t wheat straw), and sugars recovery yield in the filtrate (300 g/kg wheat straw).     

Reversible size of shear-induced multi-lamellar vesicles

We have investigated the reversibility in the shear-induced multi-lamellar vesicle (MLV) size during stepwise cycling of the shear rate by employing common rheometry, polarized light microscopy and rheo-optic techniques. We thus address the question whether there is a true MLV steady state, irrespective of history. The system studied, was the nonionic surfactant triethylene glycol decyl ether (C₁₀E₃) with a concentration of 40 wt.% in D₂O and a constant temperature of 25°C. It was found that the MLV size varies reversibly with varying shear rate, and hence there exists a true steady state in the presence of shear flow. The experimental observations of reversibility are however restricted to higher shear rates. Because the transformation of the size results from the shear strain, the process is very slow at lower shear rates, where the steady state cannot be reached within a reasonable experimental time.     

Ab initio potential energy surface, variational transition state theory, and quasiclassical trajectory studies of the F+CH4-->HF+CH3 reaction

In this work we present a study of the F+CH(4)-->HF+CH(3) reaction (DeltaHdegrees(298 K)=-32.0 kcal mol(-1)) using different methods of the chemical reaction theory. The ground potential energy surface (PES) is characterized using several ab initio methods. Full-dimensional rate constants have been calculated employing the variational transition state theory and using directly ab initio data. A triatomic analytical representation of the ground PES was derived from ab initio points calculated at the second- and fourth-order M?ller-Plesset levels with the 6-311+G(2df,2pd) basis set, assuming the CH(3) fragment to be a 15 a.m.u. pseudoatom in the fitting process. This is suggested from experiments that indicate that the methyl group is uncoupled to the reaction coordinate. A dynamics study by means of the quasiclassical trajectory (QCT) method and employing this analytical surface was also carried out. The experimental data available on the HF internal states distributions are reproduced by the QCT results. Very recent experimental information about the reaction stereodynamics is also borne out by our QCT calculations. Comparisons with the benchmark F+H(2) and analogous Cl+CH(4) reactions are established throughout.     

RNA integrity as a quality indicator during the first steps of RNP purifications : A comparison of yeast lysis methods

Background  

The completion of several genome-sequencing projects has increased our need to assign functions to newly identified genes. The presence of a specific protein domain has been used as the determinant for suggesting a function for these new genes. In the case of proteins that are predicted to interact with mRNA, most RNAs bound by these proteins are still unknown. In yeast, several protocols for the identification of protein-protein interactions in high-throughput analyses have been developed during the last years leading to an increased understanding of cellular proteomics. If any of these protocols or similar approaches shall be used for the identification of mRNA-protein complexes, the integrity of mRNA is a critical factor.