Complex formation of isocytosine tautomers with PdII and PtII

Isocytosine (ICH) exists in solution as two major tautomers, the keto form with N1 carrying a proton (1a) and the keto form with N3 being protonated (1b). In water, 1a and 1b exist in equilibrium with almost equal amounts of both forms present. Reactions with a series of Pd(II) and Pt(II) am(m)ine species such as (dien)Pd(II), (dien)Pt(II), and trans-(NH(3))(2)Pt(II) reveal, however, a distinct preference of these metals for the N3 site, as determined by (1)H NMR spectroscopy. Individual species have been identified by the pD dependence of the ICH resonances. pK(a) values (calculated for H(2)O) for deprotonation of the individual tautomers complexes are 6.5 and 6.4 for the N3 linkage isomers of dienPd(II) and dienPt(II), respectively, as well as 6.2 and 6.0 for the N1 linkage isomers. The dimetalated species [(dienM)(2)(IC-N1,N3)](3+) (M = Pd(II) or Pt(II)) are insensitive over a wide range of pD. The crystal structure analysis of [(dien)Pd(ICH-N3)](NO(3))(2) is reported. Ab initio calculations have been performed for tautomer compounds of composition [(NH(3))(3)Pt(ICH)](2+), cis- and trans-[(NH(3))(2)PtCl(ICH)](+), as well as trans-[(NH(3))(2)Pt(ICH)(2)](2+). Without exception, N3 linkage isomers are more stable, in agreement with experimental findings. As to the reasons for this binding preference, an NBO (natural bond orbital) analysis for [(NH(3))(3)Pt(ICH-N3)](2+)strongly suggests that intramolecular hydrogen bonding between trans-positioned NH(3) ligands and the two exocyclic groups of the ICH is of prime importance. The calculations furthermore show a marked pyramidalization of the NH(2) group of ICH in the complex once the heterocyclic ligand forms a dihedral angle <90 degrees with the Pt coordination plane.     

Colorimetric method for the determination of vanadium with tannic acid in water and oils

A new spectrophotometric method was developed to determine vanadium using tannic acid as a complexing reagent to form a coloured reaction product which can easily be extracted by 1-pentanol in the presence of cetylpyridinium. The developed method can successfully be applied to determine trace levels of 10 ng/ml of vanadium in natural waters without any preconcentration step. It can also determine less than 1 mg/kg of vanadium in edible oils and petroleum products.     

Nucleation mechanisms and speciation of metal oxide clusters

The self-assembly mechanisms of polyoxometalates (POMs) are still a matter of discussion owing to the difficult task of identifying all the chemical species and reactions involved. We present a new computational methodology that identifies the reaction mechanism for the formation of metal-oxide clusters and provides a speciation model from first-principles and in an automated manner. As a first example, we apply our method to the formation of octamolybdate. In our model, we include variables such as pH, temperature and ionic force because they have a determining effect on driving the reaction to a specific product. Making use of graphs, we set up and solved 2.8 × 10⁵ multi-species chemical equilibrium (MSCE) non-linear equations and found which set of reactions fitted best with the experimental data available. The agreement between computed and experimental speciation diagrams is excellent. Furthermore, we discovered a strong linear dependence between DFT and empirical formation constants, which opens the door for a systematic rescaling.

The self-assembly mechanisms of polyoxometalates (POMs) are still a matter of discussion owing to the difficult task of identifying all the chemical species and reactions involved. The POMSimulator deals with that complexity in an automated manner.     

Dynamics of an enzymatic substitution reaction in haloalkane dehalogenase

Reactive flux molecular dynamics simulations have been carried out using a combined QM/MM potential to study the dynamics of the nucleophilic substitution reaction of dichloroethane by a carboxylate group in haloalkane dehalogenase and in water. We found that protein dynamics accelerates the reaction rate by a factor of 2 over the uncatalyzed reaction. Compared to the thermodynamic effect in barrier reduction, protein dynamic contribution is relatively small. However, analyses of the friction kernel reveal that the origins of the reaction dynamics in water and in the enzyme are different. In aqueous solution, there is significant electrostatic solvation effect, which is reflected by the slow reorganization relaxation of the solvent. On the other hand, there is no strong electrostatic coupling in the enzyme and the major effect on reaction coordinate motion is intramolecular energy relaxation.     

Fluorescence immunoassay for angiotensin I

A heterogeneous fluorescence immunoassay for angiotensin I is described. Fluorescein isothiocyanate (FITC) is used as fluorescent label; it is covalently linked to angiotensin I by reacting in pH 9.2 carbonate buffer at 18°C for 24 h. A Sephadex G-10 gel filtration column permits separation of conjugate from excess of FITC. The assay is applied to 4–40 ng ml^?1 angiotensin I, with a relative standard deviation of 5%.     

Exploring the self-assembly of dumbbell-shaped polyoxometalate hybrids,from molecular building units to nanostructured soft materials

The formation of hierarchical nanostructures using preformed dumbbell-like species made of covalent organic–inorganic polyoxometalate (POM)-based hybrids is herein described. In this system, the presence of charged subunits (POM, metal linkers, and counter ions) in the complex molecular architecture can drive their aggregation, which results from a competition between the solvation energy of the discrete species and intermolecular electrostatic interactions. We show that the nature of the POM and the charge of the metal linker are key parameters for the hierarchical nanoorganization. The experimental findings were corroborated with a computational investigation combining DFT and molecular dynamics simulation methods, which outlines the importance of solvation of the counter ion and POM/counter ion association in the aggregation process. The dumbbell-like species can also form gels, in the presence of a poorer solvent, displaying similar nanoorganization of the aggregates. We show that starting from the designed molecular building units whose internal charges can be controlled by redox trigger we can achieve their implementation into soft nanostructured materials through the control of their supramolecular organization.

The formation of hierarchical nanostructures using supramolecular dumbbell-like species made of organic–inorganic polyoxometalate-based hybrids is investigated by combination of SAXS and computational methods.     

Click and count: specific detection of acid ceramidase activity in live cells

The use of intact cells in medical research offers a number of advantages over employing cell-free systems. In diagnostics, cells isolated from liquid biopsies can be directly used, speeding up the time of analysis and diminishing the risk of protein degradation by sample manipulation. In drug discovery, studies in live cells take into account aspects neglected in cell-free systems, such as uptake, metabolization, and subcellular concentration by compartmentalization of potential drug candidates. Therefore, probes for studies in cellulo are of paramount importance. Acid ceramidase (AC) is a lysosomal enzyme that hydrolyses ceramides into sphingoid bases and fatty acids. The essential role of this enzyme in the outburst and progress of several diseases, some of them still incurable, is well sustained. Despite the great clinical relevance of AC as a biomarker and therapeutic target, the specific monitoring of AC activity in live cells has remained elusive due to the concomitant existence of neutral and alkaline ceramidases. In this work, we report that 1-deoxydihydroceramides are exclusively hydrolysed by AC. Using N-octanoyl-18-azidodeoxysphinganine as a probe and a BODIPY-substituted bicyclononyne, we show the click-reliant predominant staining of lysosomes, with extra-lysosomal labeling also occurring in some cells. Importantly, using pharmacological and genetic tools together with high resolution mass spectrometry, we demonstrate that both lysosomal and extra-lysosomal staining are AC-dependent. These findings are translated into the specific flow cytometry monitoring of AC activity in intact cells, which fills an important gap in the field of diseases linked to altered AC activity.

The use of intact cells in medical research offers a number of advantages over employing cell-free systems.     

Structural distortion,charge modulation and local anisotropies in magnetite below the Verwey transition using resonant X‐ray scattering

The pattern of charge modulations and local anisotropies below the Verwey transition has been determined and quantified in high‐quality Fe₃O₄ single crystals and thin films grown on MgO by using resonant X‐ray scattering at the Fe K‐edge. The energy, polarization and azimuthal angle dependencies of an extensive set of reflections with potential sensitivity to charge or local anisotropy orderings have been analyzed to explore their origins. A charge disproportion on octahedral B sites of 0.20 ± 0.05 e^? with [0 0 1] and cubic periodicities has been confirmed, while no significant charge disproportion has been obtained with [0 0 1/2] cubic periodicity. Additional charge modulations in the monoclinic a–b plane are also present. In addition, the occurrence of new forbidden (1, 1, 0) and (0, 0, 2n + 1/2) cubic reflections that arise from the anisotropy of the local structure around different tetrahedral and octahedral Fe atoms is shown. This complex pattern of weak charge modulations and local anisotropies is fully compatible with the low‐temperature crystal structure refined in the non‐polar C2/c space group and disproves any bimodal charge disproportion of the octahedral Fe atoms.