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.     

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.     

The Effect of Gluconate and EDTA on Thorium Solubility Under Simulated Cement Porewater Conditions

α-Hydroxy carboxylate ligands like gluconate or polyaminocarboxylate ligands such as ethylenediaminetetraacetate (EDTA) are frequently used in decontamination procedures at nuclear power plants. The presence of these organic substances among nuclear wastes could enhance the solubility of actinides by forming soluble complexes. Thermodynamic data on the stability of gluconate and EDTA with actinides are essential to predict their increase in mobility, especially in high pH systems characteristic of cement environments of a nuclear waste repository. In this work, the solubility of thorium oxyhydroxide in the presence of gluconate and EDTA has been studied. The results highlight the key role of these organics in increasing the solubility of thorium at pH_c = 12. The presence of calcium at concentrations below 10^?2 mol·dm^?3 (characteristic of cement porewaters corresponding to cement compositions at the second degradation stage) does not seem to affect significantly the thorium solubility under the studied conditions.     

Aryl‐Copper(III)‐Acetylides as Key Intermediates in CCsp Model Couplings under Mild Conditions

The mechanism of copper‐mediated Sonogashira couplings (so‐called Stephens–Castro and Miura couplings) is not well understood and lacks clear comprehension. In this work, the reactivity of a well‐defined aryl‐Cu^III species ( 1 ) with p‐R‐phenylacetylenes (R=NO₂, CF₃, H) is reported and it is found that facile reductive elimination from a putative aryl‐Cu^III‐acetylide species occurs at room temperature to afford the C_aryl?C_sp coupling species ( I_R ), which in turn undergo an intramolecular reorganisation to afford final heterocyclic products containing 2H‐isoindole ( P , P , P_Ha ) or 1,2‐dihydroisoquinoline ( P_Hb ) substructures. Density Functional Theory (DFT) studies support the postulated reductive elimination pathway that leads to the formation of C?C_sp bonds and provide the clue to understand the divergent intramolecular reorganisation when p‐H‐phenylacetylene is used. Mechanistic insights and the very mild experimental conditions to effect C_aryl?C_sp coupling in these model systems provide important insights for developing milder copper‐catalysed C_aryl?C_sp coupling reactions with standard substrates in the future.     

BSE control: detection of gelatine-derived peptides in animal feed by mass spectrometry

The epidemic of bovine spongiform encephalopathy (BSE) is thought to have resulted from feeding scrapie-infected sheep to cattle. This has led to a ban of feeding animals with "processed animal protein"(PAP). We report a novel approach for the mass spectrometric detection of PAP contamination in animal feedstuffs by detecting gelatine, a derivative of the major animal protein collagen. A method was developed to hydrolyse gelatine standards with hydrochloric acid, followed by detection of the derived hydrolytic peptides at m/z 828, 915, 957 and 1044 by matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF MS) and liquid chromatography electrospray ionisation mass spectrometry (LC-ESI-MS-MS). The marker peptides can be detected at concentrations of 100 ng ml(-1) gelatine in water with MALDI. The procedure was adapted to obtain a suitable peptide map of gelatine extracted from spiked feed. The ratio of signal area of the gelatine-derived peptide at m/z 1044 to the internal standard at m/z 556 is shown to relate to the total amount of gelatine present in the sample.     

Modular amino alcohol ligands containing bulky alkyl groups as chiral controllers for Et2Zn addition to aldehydes: illustration of a design principle

A new family of enantiomerically pure (1S,2R)-1-alkyl-2-(dialkylamino)-3-(R-oxy)-1-propanols containing a very bulky alkyl substituent (tert-butyl or 1-adamantyl) on their hydrocarbon chains has been synthesized from the corresponding enantiopure epoxy alcohols, arising from the catalytic Sharpless epoxidation, by protection of the primary hydroxy group and subsequent regioselective ring opening of the epoxide by a secondary cyclic amine (C-2 attack). The performance of these amino alcohols as ligands for the catalytic enantioselective addition of diethylzinc to benzaldehyde has been studied, with enantioselectivities of 92-96% being recorded. The best performing ligands, those with a bulky R-oxy group, also depict a convenient activity and selectivity profile in the addition of Et(2)Zn to a representative family of aldehydes. An anomalous structure/enantioselectivity relationship of some ligands in the tert-butyl series has been studied using PM3 calculations, and conclusions have been drawn on the possible effects of including in modular designs structural fragments giving rise to a variety of rotameric transition states.