Ru-Controlled Thymine Tautomerization Frozen by a k1(O)-, k2(N,O)-Metallacycle: An Experimental and Theoretical Approach.

The reaction of mer-(Ru(H)2(CO)(PPh3)3) (1) with one equivalent of thymine acetic acid (THAcH) unexpectedly produces the macrocyclic dimer k1(O), k2(N,O)-(Ru(CO)(PPh3)2THAc)2 (4) and, concomitantly, the doubly coordinated species k1(O), k2(O,O)-(Ru(CO)(PPh3)2THAc) (5). The reaction promptly forms a complicated mixture of Ru-coordinated mononuclear species. With the aim of shedding some light in this context, two plausible reaction paths were proposed by attributing the isolated or spectroscopically intercepted intermediates on the basis of DFT-calculated energetic considerations. The cleavage of the sterically demanding equatorial phosphine in the mer-species releases enough energy to enable self-aggregation, producing the stable, symmetric 14-membered binuclear macrocycle of 4. The k1-acetate iminol (C=N-OH) unit of the mer-tautomer k1(O)-(Ru(CO)(PPh3)2(THAc)) (2) likely exhibits a stronger nucleophilic aptitude than the prevalent N(H)-C(O) amido species, thus accomplishing extra stabilization through concomitant k2(N,O)-thymine heteroleptic side-chelation. Furthermore, both the ESI-Ms and IR simulation spectra validated the related dimeric arrangement in solution, in agreement with the X-ray determination of the structure. The latter showed tautomerization to the iminol form. The 1H NMR spectra in chlorinated solvents of the kinetic mixture showed the simultaneous presence of 4 and the doubly coordinated 5, in rather similar amounts. THAcH added in excess preferentially reacts with 2 or trans-k2(O,O)-(RuH(CO)(PPh3)2THAc) (3) rather than attacking the starting Complex 1, promptly forming the species of 5. The proposed reaction paths were inferred by spectroscopically monitoring the intermediate species, for which the results were strongly dependent on the of conditions the reaction (stoichiometry, solvent polarity, time, and the concentration of the mixture). The selected mechanism proved to be more reliable, due to the final dimeric product stereochemistry.

Ab Initio Metadynamics Simulations of Hexafluoroisopropanol Solvent Effects: Synergistic Role of Solvent H-Bonding Networks and Solvent-Solute C-H/π Interactions.

The solvent effects in Friedel-Crafts cycloalkylation of epoxides and Cope rearrangement of aldimines were investigated by using ab initio molecular dynamics simulations. Explicit molecular treatments were applied for both reactants and solvents. The reaction mechanisms were elucidated via free energy calculations based on metadynamics simulations. The results reveal that both reactions proceed in a concerted fashion. Key solvent-substrate interactions are identified from the structures of transition states with explicit solvent molecules. The remarkable promotion effect of hexafluoroisopropanol solvent is ascribed to the synergistic effect of H-bonding networks and C-H/π interactions with substrates.

Sphingolipid hydroxylation in mammals, yeast and plants - An integrated view.

This review is focused on sphingolipid backbone hydroxylation, a small but widespread structural feature with profound impact on membrane biophysical properties. We start by summarizing sphingolipid metabolism in mammalian cells, yeast and plants, focusing on how distinct hydroxylation patterns emerge in different eukaryotic kingdoms. Then, a comparison of the biophysical properties in membrane model systems and cellular membranes from diverse organisms is made. From an integrative perspective, these results can be rationalized considering that superficial hydroxyl groups in the backbone of sphingolipids (by intervening in the H-bond network) alter the balance of favorable interactions between membrane lipids. They may strengthen the bonding or compete with other hydroxyl groups, in particular the one of membrane sterols. Different sphingolipid hydroxylation patterns can stabilize/disrupt specific membrane domains or change whole plasma membrane properties, and therefore be important in the control of protein distribution, function and lateral diffusion and in the formation and overtime stability of signaling platforms. The recent examples explored throughout this review unveil a potentially key role for sphingolipid backbone hydroxylation in both physiological and pathological situations, as it can be of extreme importance for the proper organization of cell membranes in mammalian cells, yeast and, most likely, also in plants.

From chlorite dismutase towards HemQ - the role of the proximal H-bonding network in haeme binding.

Chlorite dismutase (Cld) and HemQ are structurally and phylogenetically closely related haeme enzymes differing fundamentally in their enzymatic properties. Clds are able to convert chlorite into chloride and dioxygen, whereas HemQ is proposed to be involved in the haeme b synthesis of Gram-positive bacteria. A striking difference between these protein families concerns the proximal haeme cavity architecture. The pronounced H-bonding network in Cld, which includes the proximal ligand histidine and fully conserved glutamate and lysine residues, is missing in HemQ. In order to understand the functional consequences of this clearly evident difference, specific hydrogen bonds in Cld from 'Candidatus Nitrospira defluvii' (NdCld) were disrupted by mutagenesis. The resulting variants (E210A and K141E) were analysed by a broad set of spectroscopic (UV-vis, EPR and resonance Raman), calorimetric and kinetic methods. It is demonstrated that the haeme cavity architecture in these protein families is very susceptible to modification at the proximal site. The observed consequences of such structural variations include a significant decrease in thermal stability and also affinity between haeme b and the protein, a partial collapse of the distal cavity accompanied by an increased percentage of low-spin state for the E210A variant, lowered enzymatic activity concomitant with higher susceptibility to self-inactivation. The high-spin (HS) ligand fluoride is shown to exhibit a stabilizing effect and partially restore wild-type Cld structure and function. The data are discussed with respect to known structure-function relationships of Clds and the proposed function of HemQ as a coprohaeme decarboxylase in the last step of haeme biosynthesis in Firmicutes and Actinobacteria.