Interaction of Ca2+ with uracil and its thio derivatives in the gas phase

The structures and relative stabilities of the complexes formed by uracil and its sulfur derivatives, namely, 2-thio-, 4-thio, and 2,4-dithio-uracil when interacting with Ca(2+) in the gas phase have been analyzed by means of density functional theory (DFT) calculations carried out at the B3LYP/6-311++G(3df,2p)//B3LYP/6-31+G(d,p) level. For uracil and 2,4-dithiouracil, where the two basic sites are the same, Ca(2+) attachment to the heteroatom at position 4 is preferred. However, for the systems where both types of basic centers, a carbonyl or a thiocarbonyl group, are present, Ca(2+)-oxygen association is favored. The most stable complexes correspond to structures with Ca(2+) bridging between the heteroatom at position 2 of the 4-enol (or the 4-enethiol) tautomer and the dehydrogenated ring nitrogen, N3. The enhanced stability of these enolic forms is two-fold, on the one hand Ca(2+) interacts with two basic sites and on the other triggers a significant aromatization of the ring. Besides, Ca(2+) association has a clear catalytic effect on the tautomerization processes which connect the oxo-thione forms with the enol-enethiol tautomers. Hence, although the enol-enethiol tautomers of uracil and its thio derivatives should not be observed in the gas phase, the corresponding Ca(2+) complexes are the most stable species and should be accessible, because the tautomerization barriers are smaller than the Ca(2+) binding energies.     

Activation of two C-H bonds of NHC N-methyl groups on triosmium and triruthenium carbonyl clusters

The thermolysis of the NHC triosmium cluster [Os3(Me2Im)(CO)11] (1a; Me2Im = 1,3-dimethylimidazol-2-ylidene) in toluene at reflux temperature sequentially affords the edge-bridged cluster [Os3(micro-H)(micro-kappa2-MeImCH2)(CO)10] () and the face-capped derivative [Os3(micro-H)2(micro3-kappa2-MeImCH)(CO)9] (3a). These products result from the sequential oxidative addition of one (2a) and two (3a) N-methyl C-H bonds of the original NHC ligand. The related face-capped triruthenium cluster [Ru3(micro-H)2(micro3-kappa2-MeImCH)(CO)9] (3b) has been prepared by heating the NHC triruthenium cluster [Ru3(Me2Im)(CO)11] (1b) in THF at reflux temperature. In this case, the pentanuclear derivatives [Ru5(Me2Im)(micro4-kappa2-CO)(CO)14] (4b) and [Ru5(Me2Im)2(micro4-kappa2-CO)(CO)13] (5b) are minor reaction products, but a ruthenium cluster analogous to has not been obtained. The face-capped oxazole-derived NHC triruthenium cluster [Ru3(micro-H)2(micro3-kappa2-OxCH)(CO)9] (3c; MeOx = N-methyloxazol-2-ylidene) is the only isolated product of the thermolysis of [Ru3(MeOx)(CO)11] (1c) in THF at reflux temperature.     

A theoretical study of medium effects on the structure of the glycine analogue aminomethylphosphonic acid

alpha-Aminophosphonic acids are analogues of natural alpha-aminoacids and very promising agents for use in various pharmaceutical applications. However, in contrast to the numerous theoretical investigations on the structure of natural alpha-aminoacids, only very few studies on alpha-aminophosphonic acids have been performed. In the present work, we report a detailed investigation of the simplest compound, the glycine analogue aminomethylphosphonic acid (AMPA), by means of quantum mechanical calculations at the B3LYP/6-311++G(3df,2p)//B3LYP/6-31+G(d,p) and MP2/6-311++G(3df,2p)//B3LYP/6-31+G(d,p) levels. We focus on the structure of the neutral species looking at the evolution of non-ionized and ionized forms from gas phase to non-polar solvents and aqueous media. Continuum and discrete-continuum solvent models have been employed to account for the effects of the environment. The discussion is centered on: (1) the geometry and relative stability of possible conformers in gas phase and aqueous solution, (2) the free energy of tautomerization in different media, (3) the role of hydrogen bonds in liquid water, and (4) the free energy of transfer from water to a hydrophobic solvent such as cyclohexane. Systematic comparison between AMPA and Gly is performed. Though both systems exhibit many similarities, some important differences have also been found that may be explained, at least in part, by the higher acidity of phosphonic acids compared to carboxylic acids. In particular, in solvents lacking hydrogen-bond formation capability, Gly derivatives should mainly exist as non-ionized molecules while the equivalent AMPA derivatives should adopt a zwitterionic structure in media with dielectric constant above 10. This might have significant environmental or biological consequences that will need to be addressed.     

Generation of time-dependent concentration profiles using a reduced-size continuous-flow manifold

A computer-controlled manifold allowing the automatic generation of concentration profiles is described. For this purpose, the sample or standard solution is placed inside a semi-closed loop to which diluent is incorporated at a given flow rate, while the solution is removed at the same flow rate and directed towards the detector. The flow manifold, which works in a similar way to the tank model, includes a membrane micropump to recirculate the solution in the semi-closed loop. For simplicity purposes in the assessment of the system, a flame atomic absorption spectrometer is used for both withdrawing liquid and detection, although the basic idea can easily be extended to other detectors. The experimental data, verified by measuring the calcium, magnesium, sodium and potassium contents of some soft drinks demonstrate that the approach is reliable and may be a basis for developing portable instruments of reduced-size.     

Determination of PASHs by various analytical techniques based on gas chromatography-mass spectrometry: application to a biodesulfurization process

Polycyclic aromatic sulphur heterocyclic (PASH) compounds, such as dibenzothiophene (DBT) and alkylated derivatives are used as model compounds in biodesulfurization processes. The development of these processes is focused on the reduction of the concentration of sulphur in gasoline and gas–oil [D.J. Monticello, Curr. Opin. Biotechnol. 11 (2000) 540], in order to meet European Union and United States directives.

The evaluation of biodesulfurization processes requires the development of adequate analytical techniques, allowing the identification of any transformation products generated. The identification of intermediates and final products permits the evaluation of the degradation process.

In this work, seven sulfurated compounds and one non-sulfurated compound have been selected to develop an extraction method and to compare the sensitivity and identification capabilities of three different gas chromatography ionization modes. The selected compounds are: dibenzothiophene (DBT), 4-methyl-dibenzothiophene (4-m-DBT), 4,6-dimethyl-dibenzothiophene (4,6-dm-DBT) and 4,6 diethyl-dibenzothiophene (4,6 de-DBT), all of which can be used as model compounds in biodesulfurization processes; as well as dibenzothiophene sulfoxide (DBTO₂), dibenzothiophene sulfone (DBTO) and 2-(2-hydroxybiphenyl)-benzenesulfinate (HBPS), which are intermediate products in biodesulfurization processes of DBT [ A. Alcon, V.E. Santos, A.B. Martín, P. Yustos, F. García-Ochoa, Biochem. Eng. J. 26 (2005) 168]. Furthermore, a non-sulfurated compound, 2-hydroxybiphenyl (2-HBP), has also been selected as it is the final product in the biodesulfurization process of DBT [A. Alcon, V.E. Santos, A.B. Martín, P. Yustos, F. García-Ochoa. Biochem. Eng. J. 26 (2005) 168].

Since, typically, biodesulfurization reactions take place in a biphasic medium, two extraction methods have been developed: a liquid–liquid extraction method for the watery phase and a solid phase extraction method for the organic phase. Recoveries of the selected compound in both media were studied. They were in the range of 80–100% for the watery and in the range of 40–60% for the organic phase, respectively.

Gas chromatography coupled to mass spectrometry (GC–MS) has been employed for the identification of these selected compounds. Three different ionization modes were applied: conventional electron impact (EI); positive chemical ionization (PCI), using methane as the reagent gas; and a recently developed ionization mode known as hybrid chemical ionization (HCI), using perfluorotri-n-butylamine as the reagent gas. Limits of detection and identification capabilities have been compared between the three analytical techniques.

The sensitivity of the three analytical techniques was studied and LOD between 0.05 and 1, between 0.09 and 2 and between 0.001 and 0.043 were achieved for PCI, EI and HCI, respectively.

The developed method was applied in samples from a biodesulfurization process. The biodesulfurization reactions were conducted in resting cell operation mode, using Erlenmeyer flasks or an agitated tank bioreactor. The microorganism employed was Pseudomonas putida CECT 5279. The reaction was performed under controlled air flow, stirring and temperature conditions.     

Wavelet neural networks to resolve the overlapping signal in the voltammetric determination of phenolic compounds

Three phenolic compounds, i.e. phenol, catechol and 4-acetamidophenol, were simultaneously determined by voltammetric detection of its oxidation reaction at the surface of an epoxy-graphite transducer. Because of strong signal overlapping, Wavelet Neural Networks (WNN) were used in data treatment, in a combination of chemometrics and electrochemical sensors, already known as the electronic tongue concept. To facilitate calibration, a set of samples (concentration of each phenol ranging from 0.25 to 2.5mM) was prepared automatically by employing a Sequential Injection System. Phenolic compounds could be resolved with good prediction ability, showing correlation coefficients greater than 0.929 when the obtained values were compared with those expected for a set of samples not employed for training.     

Seltenerdhalogenide Ln4X5Z. Teil 1: C und/oder C2 in Ln4X5Z

Rare Earth Halides Ln₄X₅Z. Part 1: C and/or C₂ in Ln₄X₅Z The compounds Ln₄X₅C_n (Ln = La, Ce, Pr; X = Br, I and 1.0 < n < 2.0) are prepared by the reaction of LnX₃, Ln metal and graphite in sealed Ta‐ampoules at temperatures 850 °C < T < 1050 °C. They crystallize in the monoclinic space group C2/m. La₄I₅C_1.5: a = 19.849(4) Å, b = 4.1410(8) Å, c = 8.956(2) Å, β = 103.86(3)°, La₄I₅C_2.0: a = 19.907(4) Å, b = 4.1482(8) Å, c = 8.963(2) Å, β = 104.36(3)°, Ce₄Br₅C_1.0: a = 18.306(5) Å, b = 3.9735(6) Å, c = 8.378(2) Å, β=104.91(2)°, Ce₄Br₅C_1.5: a = 18.996(2) Å, b = 3.9310(3) Å, c = 8.282(7) Å, β = 106.74(1)°, Pr₄Br₅C_1.3: a = 18.467(2) Å, b = 3.911(1) Å, c = 8.258(7) Å, β = 105.25(1)° and Pr₄Br₅C_1.5: a = 19.044(2) Å, b = 3.9368(1) Å, c = 8.254(7) Å, β = 106.48(1)°. In the crystal structure the lanthanide metals are connected to Ln₆‐octahedra centered by carbon atoms or C₂‐groups. The Ln₆‐octahedra are condensed via opposite edges to chains and surrounded by X atoms which interconnect the chains. A part n of isolated C‐atoms is substituted by 1‐n C₂‐groups. The C‐C distances range between 1.26 and 1.40Å. In the ionic formulation (Ln³⁺)₄(X^?)₅(C^4?)_n(C₂^m?)_1?n·e^? with 0 < n < 1 and m = 2, 4, 6 (C₂^2?, C₂^4? C₂^6?), there are 1 < e^? < 5 electrons centered in metal‐metal bonds.     

Protein extraction from Phoenix dactylifera L. leaves, a recalcitrant material, for two-dimensional electrophoresis

This work was aimed at optimizing a protein extraction procedure for date palm (Phoenix dactylifera L.) leaves, a highly recalcitrant plant tissue for 2-DE. Five protein extraction protocols based on different protein precipitation agents (TCA/acetone vs. phenol (Ph) methods) and protein resolubilization methods (physical treatments, e.g., sonication, shaking and/or heating) were tested. Ph/SDS extraction with methanol/ammonium acetate precipitation, followed by DOC preincubation and TCA/acetone precipitation and, finally, solubilization by shaking in rehydration solution was found to be the best protein extraction method. We conclude that DOC with TCA/acetone precipitation step eliminates interfering compounds, thus allowing efficient resolubilization of date palm leaf proteins. This method could be appropriate for proteomic studies such as date palm colonization by entomopathogenic fungi.     

High-resolution 2-DE for resolving proteins, protein adducts and complexes in plasma

A 2-DE system has been devised in which proteins are first separated in their native state followed by separation according to mass under denaturing conditions (Nat/SDS-PAGE). Hydrophilic properties of the gel and the presence of dihydroxybisacrylamide in the first dimension allowed a good resolution for high-molecular-weight proteins and maintained interactions. With this method 252 plasma spots have been resolved and 140 have been characterized by MS as isoforms of 60 proteins, a relevant part of which (12) were not detected by traditional 2-D gels or by other nondenaturing 2-D techniques. The list includes complement factors (C4d, C7), coagulation factors (coagulation factor II, fibrin beta), apolipoproteins (apolipoprotein B) and cell debris (vinculin, gelsolin, tropomyosin, dystrobrevin beta, fibrinectin I). Nat/SDS PAGE also allowed separation of nicked forms of albumin, Apo B100 and alpha2-macroglobulin and showed the presence of atypical albumin adducts corresponding to post-translational and oxidation products. Our system provides therefore new tools for resolving proteins, protein aggregates and complexes and amplifies the potentiality of traditional electrophoretic analysis.     

Preparation and evaluation of butyl acrylate-based monolithic columns for CEC using ammonium peroxodisulfate as a chemical initiator

Acrylate-ester-based monoliths for CEC using peroxodisulfate as a chemical initiator were prepared. The influence of two ternary porogenic solvents on the physical and chromatographic properties of butyl acrylate monolithic stationary phases was investigated. The composition and the ratio of porogenic solvent were adjusted to obtain highly permeable rigid monoliths with adequate column efficiency. Among the prepared butyl acrylate monoliths, those polymerized from a ternary porogenic solvent of acetonitrile/ethanol/water exhibited the most promising performance with a minimum plate height for naphthalene of 10.5 microm and a bed permeability of 7.3 x 10(-14) m(2). A comparison in terms of efficiency and permeability with thermal and UV initiation using alpha,alpha'-AIBN was also performed. The resulting monolithic stationary phases were evaluated in terms of reproducibility, giving RSD values below 5.1% in the electrochromatographic properties studied.