Analysis of electron delocalization in aromatic systems: individual molecular orbital contributions to para-delocalization indexes (PDI)

Our research group has recently defined two new aromaticity indexes based on the analysis of electron delocalization in aromatic species using the quantum theory of atoms-in-molecules. One of these indexes is the para-delocalization index (PDI) that measures the electronic delocalization between para-related carbon atoms in six-membered rings. In this paper, we show that this index can be partitioned into individual molecular orbital contributions. We have applied this PDI decomposition to several polycyclic aromatic hydrocarbons showing that this partitioning provides new insight into the origin of aromaticity.     

New insights into the reaction mechanism catalyzed by the glutamate racemase enzyme: pH titration curves and classical molecular dynamics simulations

The mechanism of the reactions catalyzed by the pyridoxal-phosphate-independent amino acid racemases and epimerases faces the difficult task of deprotonating a relatively low acidicity proton, the amino acid's alpha-hydrogen, with a relatively poor base, a cysteine. In this work, we propose a mechanism for one of these enzymes, glutamate racemase (MurI), about which many controversies exist, and the roles that its active site residues may play. The titration curves and the pK1/2 values of all of the ionizable residues for different structures leading from reactants to products have been analyzed. From these results a concerted mechanism has been proposed in which the Cys70 residue would deprotonate the alpha-hydrogen of the substrate while, at the same time, being deprotonated by the Asp7 residue. To study the consistency of this mechanism classical molecular dynamics (MD) simulations have been carried out along with pK1/2 calculations on the MD-generated structures.     

A Colorimetric Sensor Array for the Detection of the Date‐Rape Drug γ‐Hydroxybutyric Acid (GHB): A Supramolecular Approach

γ‐Hydroxybutyric acid (GHB), a colourless, odourless and tasteless chemical, has become one of the most dangerous illicit drugs of abuse today. At low doses, this drug is a central nervous system depressant that reduces anxiety and produces euphoria and relaxation, sedating the recipient. There is an urgent need for simple, easy‐to‐use sensors for GHB in solution. Here, we present a colorimetric sensor array based on supramolecular host–guest complexes of fluorescent dyes with organic capsules (cucurbiturils) for the detection of GHB.     

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.     

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.     

Comparative study of the prereactive protein kinase A Michaelis complex with Kemptide substrate

In the present work we have modeled the Michaelis complex of the cyclic-Adenosine Monophosphate Dependent (cAMD) Protein Kinase A (PKA) with Mg(2)ATP and the heptapeptide substrate Kemptide by classical molecular dynamics. The chosen synthetic substrate is relevant for its high efficiency and small size, and it has not been used in previous theoretical studies. The structural analysis of the data generated along the 6 ns simulation indicates that the modeled substrate-enzyme complex mimics the substrate binding pattern known for PKA. The values of the average prereactive distances obtained from the simulation do not exclude any of the two limiting situations proposed as mechanisms in the literature for the phosphorylation reaction (dissociative and associative) because the system oscillates between configurations compatible with each of them. Furthermore, the results obtained for the average interaction distances between active site residues concord in suggesting the plausibility of an alternative third reaction mechanism.     

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.     

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.     

Influence of self-assembly of amphiphilic imidazolium ionic liquids on their host–guest complexes with cucurbit[n]urils

Two symmetric amphiphilic imidazolium ionic liquids having ω-undecenyl chains form supramolecular complexes with CB[7] and CB[8] in water as revealed by ¹H NMR spectroscopy and MALDI-MS. Binding constants in the range 10⁴ to 10⁵ M^?1 were estimated from the conductivity measurements for the 1:1 complexes of these imidazolium ionic liquids with CB[7] and CB[8]. Radical initiated polymerization of these host–guest complexes at concentrations above the critical self-assembly concentration of imidazolium ionic liquids to form liposomes, destroys completely (CB[7]) or partially (CB[8]) the host–guest ionic liquid@CB[n] complex; this behaviour was proved by titration with acridine orange tricyclic dye, of CB[n]s in the colloidal solutions of the liposomes before and after performing dialysis to remove free CB[n]s. Thus, the increase in the fluorescence emission of acridine orange by CB[7] is not observed if the polymerized ionic liquid@CB[7] complex is submitted to dialysis to remove uncomplexed CB[7]. Analogous study by titration of absorbance change of acridine orange solutions caused by CB[8], reveals only a partial destruction of the host–guest complex by self-assembly of amphiphilic ionic liquid above the critical self-assembly concentration. The results obtained have been rationalized considering that the driving force for the formation of supramolecular ionic liquid@CB[n] complexes is a hydrophobic interaction between the apolar alkenyl chain and the cucurbituril interior cavity and that these hydrophobic interactions are disturbed when self-assembly leading to liposomes occurs.