Profiling of N-acyl-homoserine lactones by liquid chromatography coupled with electrospray ionization and a hybrid quadrupole linear ion-trap and Fourier-transform ion-cyclotron-resonance mass spectrometry (LC-ESI-LTQ-FTICR-MS)

A method for the comprehensive profiling of the N-acyl-homoserine lactone (AHL) family of bacterial quorum-sensing molecules is presented using liquid chromatography (LC) coupled to a hybrid quadrupole linear ion trap (LTQ) and Fourier-transform ion-cyclotron-resonance mass spectrometer (FTICR). We demonstrate an increase in signal intensity in MS with electrospray ionization (ESI) of the protonated molecules, [M + H](+), by using acetonitrile (ACN) instead of methanol (MeOH) as the organic solvent under the conditions in which the samples were supplied to the probe by direct infusion at constant flow rates. The presence of ACN prevents the formation of methanol adducts such as [M + MeOH + H](+) and [M + MeOH + Na](+), while also lowering the signal intensity of sodiated [M + Na](+) ions. Sensitivity of these signaling molecules in terms of signal-to-noise ratio (S/N) using low-resolution LTQ-MS and high-resolution FTICR-MS were compared under reversed-phase (RP) LC separations with ESI interface. Special emphasis was paid to the choice of the separation column, its elution conditions and detection of the major AHL compounds produced by the Serratia liquefaciens strain ATCC 27592. The most promising results were obtained using a RP C16-amide column eluted with a linear mobile phase gradient ACN/H(2)O containing 0.1% formic acid. The whole set of AHL homologs in bacterial extracts was detected in the extracted-ion chromatographic (XIC) mode, and the calculations of molecular formulae were performed by including the isotopic pattern. This mode of displaying data, with a very narrow mass-to-charge ratio window (i.e. +/- 0.0010 as m/z unit) around each selected ion, has allowed the identification of all the eight known homoserine lactones, viz. C(4)-HSL, 3-oxo-C(6)-HSL, C(6)-HSL, 3-oxo-C(8)-HSL, C(8)-HSL, C(10)-HSL, C(12)-HSL and C(14)-HSL. In addition, at least four uncommon signaling mediators previously unreported, namely, 3-oxo-C(10:1)-HSL, 3-oxo-C(11:2)-HSL, 3-oxo-C(13:2)-HSL and 3-OH-C(16)-HSL, were identified and characterized; their roles in cell-to-cell communication has to be elucidated.     

The onset of calcium carbonate nucleation: a density functional theory molecular dynamics and hybrid microsolvation/continuum study

Density functional theory (Perdew-Burke-Ernzerhof) based methods have been used to study the structure and hydration environment of the building blocks of CaCO 3 in aqueous solutions of calcium bicarbonate and calcium carbonate. Car-Parrinello molecular dynamics simulations of Ca(2+)/CO3(2-) and Ca (2+)/HCO3(-) in explicit water were performed to investigate the formation of CaCO3 and the hydration shell of the solvated hetero-ion pair. Our simulations show that the formation of the monomer of CaCO3 occurs with an associative mechanism and that the dominant building block of calcium (bi)carbonate in aqueous solution is Ca[eta(1)-(H)CO3](H2O)5, i.e., the preferred hydration number is five, while the (bi)carbonate is coordinated to the calcium in a monodentate mode. This result agrees with static calculations, where a hybrid approach using a combination of explicit solvent molecules and a polarizable continuum model has been applied to compute the solvation free energies of calcium bicarbonate species. Furthermore, the discrete-continuum calculations predict that the Ca(HCO3)2 and Ca(HCO3)3(-) species are stable in an aqueous environment preferentially as Ca(HCO3)2(H2O)4 and Ca(HCO3)3(H2O)2(-), respectively.     

Design of acidochromic dyes for facile preparation of pH sensor layers

Eight new acidochromic dyes have been synthesised that can be used for optically monitoring pH in the range from 3 to 12. Their corresponding pK(a) values have been both measured and calculated theoretically by means of density functional theory. The synthesis of these new dyes is facile without the need for chromatographic purification. The dyes can be covalently linked to polymers containing hydroxyl functions such as cellulose, polyurethane hydrogel, and hydroxyalkyl methacrylate. The resulting sensor layers exhibit significant colour changes both in the UV and in the visible spectral range.     

Iminyl radicals from alpha-azido o-iodoanilides via 1,5-H transfer reactions of aryl radicals: new transformation of alpha-azido acids to decarboxylated nitriles

The radical reaction of tributyltin hydride with o-iodo- N-methylanilides derived from alpha-azido acids provides an excellent access to alpha-(aminocarbonyl)iminyl radicals through 1,5-hydrogen transfer reaction of initially formed aryl radicals followed by beta-elimination of dinitrogen from ensuing alpha-azido-alpha-(aminocarbonyl)alkyl radicals. The outcoming iminyls display a peculiar tendency to form corresponding nitriles by beta-elimination of aminocarbonyl radicals.     

2-amino-1-propanol versus 1-amino-2-propanol: valence band and C 1s core-level photoelectron spectra

Valence band and C 1s core-level photoelectron spectra of S-(+)-2-amino-1-propanol (alaninol) and S-(+)-1-amino-2-propanol (isopropanolamine) have been studied by means of synchrotron radiation photoelectron spectroscopy in gas phase. The alaninol, the reduced derivative of the alanine, is a good test system of amino acid-like structures. The isopropanolamine, presenting the inversion of the two functional groups of the alaninol at the chiral carbon, offers the opportunity to study the effect of -OH and -NH(2) structural position on the photoelectron spectra. The influence of the conformational contribution on the electronic structure and the photoelectron spectra has been interpreted using density functional and ab initio theoretical calculations. Agreement has been achieved by taking into account the presence, in gas phase, of two conformers with different population ratios in both chiral systems. The C 1s core-level spectra of alaninol and isopropanolamine are reported and the peak positions of the three carbon atoms of the molecules are assigned.     

In silico binding free energy predictability by using the linear interaction energy (LIE) method: bromobenzimidazole CK2 inhibitors as a case study

Protein kinase CK2 is essential for cell viability, and its control regards a broad series of cellular events such as gene expression, RNA, and protein synthesis. Evidence of its involvement in tumor development and viral replication indicates CK2 as a potential target of antineoplastic and antiviral drugs. In this study the Linear Interaction Energy (LIE) Method with the Surface Generalized Born (SGB) continuum solvation model was used to study several bromobenzimidazole CK2 inhibitors. This methodology, developed by Aqvist, finds a plausible compromise between accuracy and computational speed in evaluating binding free energy (DeltaGbind) values. In this study, two different free binding energy models, named "CK2scoreA" and "CK2scoreB", were developed using 22 inhibitors as the training set in a stepwise approach useful to appropriately select both the tautomeric form and the starting binding position of each inhibitor. Both models are statistically acceptable. Indeed, the better one is characterized by a correlation coefficient (r2) of 0.81, and the predictive accuracy was 0.65 kcal/mol. The corresponding validation, using an external test set of 16 analogs, showed a correlation coefficient (q2) of 0.68 and a prediction root-mean-square error of 0.78 kcal/mol. In this case, the LIE approach has been proved to be an efficient methodology to rationalize the difference of activity, the key interactions, and the different possible binding modes of this specific class of potent CK2 inhibitors.     

Next-generation integrated microfluidic circuits

This mini-review provides a brief overview of recent devices that use networks of elastomeric valves to minimize or eliminate the need for interconnections between microfluidic chips and external instruction lines that send flow control signals. Conventional microfluidic control mechanisms convey instruction signals in a parallel manner such that the number of instruction lines must increase as the number of independently operated valves increases. The devices described here circumvent this "tyranny of microfluidic interconnects" by the serial encoding of information to enable instruction of an arbitrary number of independent valves with a set number of control lines, or by the microfluidic circuit-embedded encoding of instructions to eliminate control lines altogether. Because the parallel instruction chips are the most historical and straightforward to design, they are still the most commonly used approach today. As requirements for instruction complexity, chip-to-chip communication, and real-time on-chip feedback flow control arise, the next generation of integrated microfluidic circuits will need to incorporate these latest interconnect flow control approaches.     

trans-Fe(II)(H)2(diphosphine)(diamine) complexes as alternative catalysts for the asymmetric hydrogenation of ketones? A DFT study

New insights into the structural, electronic and catalytic properties of Fe complexes are provided by a density functional theory study of model as well as real [Fe(II)(H)(2)(diphosphine)(diamine)] systems. Calculations conducted using several different functionals on the trans- and cis-isomers of [Fe(II)(H)(2)(S-xylbinap)(S,S-dpen)] complexes show that, as with the [Ru(II)(H)(2)(diphosphine)(diamine)] complexes, the trans-[Fe(II)(H)(2)(diphosphine)(diamine)] complex is the more stable isomer. Analysis of the spin states of the trans-[Fe(II)(H)(2)(diphosphine)(diamine)] complexes also shows that the singlet state is significantly more stable than the triplet and the quintet, as with the [Ru(II)(H)(2)(diphosphine)(diamine)] complexes. Calculations of the catalytic cycle for the hydrogenation of ketones using two model trans-[M(II)(H)(2)(PH(3))(2)(en)] catalysts, where M = Ru and Fe, show that the mechanism of reaction as well as the activation energies are very similar, in particular: (i) the ketone/alcohol hydrogen transfer reaction occurs through the metal-ligand bifunctional mechanism, with energy barriers of 3.4 and 3.2 kcal mol(-1) for the Ru- and Fe-catalysed reactions, respectively; (ii) the heterolytic splitting of H(2) across the M[partial double bond, bottom dashed]N bond for the regeneration of the Ru and Fe catalysts has an activation barrier of 13.8 and 12.8 kcal mol(-1), respectively, and is expected to be the rate determining step for both catalytic systems. The reduction of acetophenone by trans-[M(II)(H)(2)(S-xylbinap)(S,S-dpen)] complexes along two competitive reaction pathways, shows that the intermediates for the Fe catalytic system are similar to those responsible for the high enantioselectivity of (R)-alcohol in those proposed trans-[Ru(II)(H)(2)(S-xylbinap)(S,S-dpen)] catalysed acetophenone hydrogenation reaction. Thus the high enantiomeric excess in the hydrogenation of acetophenone could, in principle, be achieved using Fe catalysts.     

On-line monitoring and active control of dye uptake in dye-sensitised solar cells

Real-time monitoring of dye loading (N3 and N719) under continuous flow conditions on TiO(2) photoanodes for dye-sensitized solar cells has been applied to quantitatively investigate dye uptake kinetics, demonstrating that static impregnation provides in all cases higher dye loading and, as a consequence, better working devices.