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.     

Novel chiral three-dimensional iron(III) compound exhibiting magnetic ordering at T(c) = 40 K

The preparation and crystal structure determination of the iron(III) compound of formula [(NH(4))(2)[Fe(2)O(ox)(2)Cl(2)].2H(2)O](n) (1) (ox = oxalate dianion) are reported here. Complex 1 crystallizes in the orthorhombic system, space group Fdd2, with a = 14.956(7) A, b = 23.671(9) A, c = 9.026(4) A, and Z = 8. The structure of complex 1 consists of the chiral anionic three-dimensional network [Fe(2)O(ox)(2)Cl(2)](2-) where the iron(III) ions are connected by single oxo and bisbidentate oxalato groups. The metal-metal separations through these bridging ligands are 3.384(2) and 5.496(2) A, respectively. Ammonium cations and crystallization water molecules are located in the helical pseudohexagonal tunnels defined by iron atoms. The longest iron-iron distance in the pseudohexagonal tunnel is 15.778(2) A whereas the shortest one is 8.734(2) A. The iron atoms are hexacoordinated: a terminal chloro ligand and five oxygen atoms, that of the oxo group and four from two cis coordinated oxalate ligands, build a distorted octahedral environment around the metal atom. The Fe-O(oxo) bond distance [1.825(2) A] is significantly shorter than the Fe(III)-O(ox) [average value 2.103(4) A] and Fe(III)-Cl bond distances [2.314(2) A]. Magnetic susceptibility measurements of 1 in the temperature range 2.0-300 K reveal the occurrence of a susceptibility maximum at 195 K and a transition toward a magnetically ordered state in the lower temperature region with T(c) = 40 K. The strong antiferromagnetic coupling through the oxo bridge (J = -46.4 cm(-1), the Hamiltonian being H = -JS(A).S(B)) accounts for the susceptibility maximum whereas a weak spin canting of approximately 0.3 degrees due to the antisymmetric magnetic exchange within the chiral three-dimensional network is responsible for the magnetic ordering. The values of coercive field (H(c)) and remnant magnetization (M(r)) obtained from the hysteresis loop of 1 at 5 K are 4000 G and 0.016 micro(B).     

Reductive ring opening of dihydrodibenzothiepine and dihydrodinaphtho-oxepine and -thiepine

The 4,4′di-tert-butylbiphenyl (DTBB)-catalysed lithiation of dihydrodibenzothiepine (1) at −78 °C for 30 min followed by reaction with a carbonyl compound [^tBuCHO, Ph(CH₂)₂CHO, PhCHO, (n-C₅H₁₁)₂CO, (CH₂)₅CO, (CH₂)₇CO, (−)-menthone] at the same temperature leads, after hydrolysis with 3 M hydrochloric acid, to sulphanyl alcohols 2. If after addition of a carbonyl compound as the first electrophile [Me₂CO, (CH₂)₅CO, (−)-menthone], the resulting dianion of type II is allowed to react at room temperature for 30 min, a second lithiation takes place to give an intermediate of type III, which by reaction with a second electrophile [Me₂CO, Et₂CO, (CH₂)₅CO, ClCO₂Et], yields, after hydrolysis, difunctionalised byphenyls 4. The cyclisation of the sulphanyl alcohol 2c under acidic conditions yields the eight-membered sulphur containing heterocycle 3. The lithiation of dihydrodinaphthoheteroepines 7 and 10 with 2.2 equiv of lithium naphthalenide in THF at −78 °C followed by reaction with different electrophiles [H₂O, D₂O, ^tBuCHO, Me₂CO, Et₂CO, (CH₂)₄CO, (CH₂)₅CO] at the same temperature leads, after hydrolysis, to unsymmetrically 2,2′-disubstituted binaphthyls 9 and 12, respectively. When the lithiation is performed with an excess of lithium in the presence of a catalytic amount of DTBB (10% molar), a double reductive cleavage takes place to give the dianionic intermediate VII, which by reaction with different electrophiles [H₂O, Me₂CO, Et₂CO, (CH₂)₄CO, (CH₂)₅CO], followed by hydrolysis with water, yields symmetrically 2,2′-disubstituted binaphthyls 8 and 11. In the case of starting from (R)- or (S)-dihydrodinaphthoheteroepines 7 and 10, these methodologies allow us to prepare enantiomerically pure compounds 8, 11 and 12.     

Molecular mechanics (MM2) and conformational analysis of compounds with N?C?O units. Parametrization of the force field and anomeric effect

A molecular mechanics force field was developed for systems bearing the N? C? O unit on the basis of 6-31G* and 4-21G “ab initio” calculations with full optimization of the geometry and experimental heats of formation. The parameters used, which implicitly included the anomeric effect, provided good geometric and energetic results, both for the compounds on which the parametrization was based and for others on which the validity of the predictions was checked.     

Molecular nitrides containing group 4 and 5 metals: single and double azatitanocubanes

Treatment of [[Ti(eta(5)-C(5)Me(5))(micro-NH)](3)(micro(3)-N)] (1) with the imido complexes [Ti(NAr)Cl(2)(py)(3)] (Ar=2,4,6-C(6)H(2)Me(3)) and [Ti(NtBu)Cl(2)(py)(3)] in toluene affords the single azatitanocubanes [[Cl(2)(ArN)Ti]( micro(3)-NH)(3)[Ti(3)(eta(5)-C(5)Me(5))(3)(micro(3)-N)]].(C(7)H(8)) (2.C(7)H(8)) and [[Cl(2)Ti](micro(3)-N)(2)(micro(3)-NH)[Ti(3)(eta(5)-C(5)Me(5))(3)(micro(3)-N)]] (3), respectively. Similar reactions of complex 1 with the niobium and tantalum imido derivatives [[M(NtBu)(NHtBu)Cl(2)(NH(2)tBu)](2)] (M=Nb, Ta) in toluene give the single azaheterometallocubanes [[Cl(2)(tBuN)M](micro(3)-N)(micro(3)-NH)(2)[Ti(3)(eta(5)-C(5)Me(5))(3)(micro(3)-N)]] (M=Nb (4), Ta (5)), both complexes react with 2,4,6-trimethylaniline to yield the analogous species [[Cl(2)(ArN)M](micro(3)-N)(micro(3)-NH)(2)[Ti(3)(eta(5)-C(5)Me(5))(3)(micro(3)-N)]].(C(7)H(8)) (Ar=2,4,6-C(6)H(2)Me(3), M=Nb (6.C(7)H(8)), Ta (7.C(7)H(8))). Also the azaheterodicubanes [M[micro(3)-N)(2)(micro(3)-NH)](2)[Ti(3)(eta(5)-C(5)Me(5))(3)(micro(3)-N)](2)].2C(7)H(8) [M=Ti (8.2C(7)H(8)), Zr (9.2C(7)H(8))], and [M[(micro(3)-N)(5)(micro(3)-NH)][Ti(3)(eta(5)-C(5)Me(5))(3)(micro(3)-N)](2)].2 C(7)H(8) (Nb (10.2C(7)H(8)), Ta (11.2C(7)H(8))) were prepared from 1 and the homoleptic dimethylamido complex [M(NMe(2))(x)] (x=4, M=Ti, Zr; x=5, M=Nb, Ta) in toluene at 150 degrees C. X-ray crystal structure determinations were performed for 6 and 10, which revealed a cube- and double-cube-type core, respectively. For complexes 2 and 4-7 we observed and studied by DNMR a rotation or trigonal-twist of the organometallic ligands [[Ti(eta(5)-C(5)Me(5))(micro-NH)](3)(micro(3)-N)] (1) and [(micro(3)-N)(micro(3)-NH)(2)[Ti(3)(eta(5)-C(5)Me(5))(3)(micro(3)-N)]](1-). Density functional theory calculations were carried out on model complexes of 2, 3, and 8 to establish and understand their structures.     

Relative stability of the2 A 1g and2 E g states of the C2H 6 + ion

Anab initio study of the relative stability for the states² A _1g and² E _g of C₂H ₆ ⁺ has been carried out. The results of the Open Shell Restricted Hartree-Fock calculations lead to assign the² A _{1 g} as the ground state of the molecule in agreement with previous SCF calculations.The correlation energy associated to both states has been calculated within the correlation hole model and the results, contrary to those obtained from Configuration Interaction calculations, do not alter qualitatively the conclusions from SCF.     

Analysis of endosulfan isomers and endosulfan sulfate in air and tomato leaves by gas chromatography with electron-capture detection and confirmation by gas chromatography-mass spectrometry

Rapid analytical methods for the determination of endosulfan isomers and endosulfan-sulfate in air and plant samples were developed. The insecticides were trapped from air using a column containing Florisil and extracted with a low volume of ethyl acetate, assisted by sonication. Pesticide residues were determined by gas chromatography with electron-capture detection using a nonpolar capillary column. Residue identities were confirmed by gas chromatography coupled with mass spectrometry. Recoveries of these compounds from air samples were always higher than 78% with an RSD lower than 11% and the detection limits obtained were at least 0.3 ng/l air. Leaf samples were homogenised with ethyl acetate and extracts cleaned-up on an aluminium oxide column. Pesticides were eluted with a hexane-ethyl acetate (80:20, v/v) mixture. Recoveries obtained from plant samples were higher than 78% with an RSD lower than 14% and detection limits in leaves were 0.02 microg/g for each pesticide. These methods were applied to study the volatilisation of endosulfan from tomato leaves under laboratory conditions. A volatilisation rate near 1% of the initial amount of endosulfan per hour was obtained during the first 24 h at room temperature.     

Rapid trace analysis of alachlor in water and vegetable samples

The use of a rapid and specific (cross-reactivity<4%) enzyme-linked immunosorbent assay (ELISA) for the determination of alachlor residues in water and vegetable samples is addressed. The analytical method consists of a fast extraction procedure followed by an optimised ELISA. The detection limit was 0.44 microg l(-1), with a linear range from 0.89 to 143.2 microg l(-1). For alachlor extraction from water samples, different solid-phase cartridges (C, Ph, C8 and C2) were assayed using MeOH as eluent. Extracts were diluted (1:4) with distilled water before ELISA. This procedure gave recoveries close to 100% with RSDs<14%. For vegetable samples, alachlor was extracted directly with MeOH and the extracts diluted 1:40 (v/v) with saline buffer prior to ELISA. The results obtained by the proposed procedure correlate well with the reference method (multiresidue extraction-GC-MS) for vegetable samples (r>0.85).