Evolutionarily conserved functional mechanics across pepsin-like and retroviral aspartic proteases

The biological function of the aspartic protease from HIV-1 has recently been related to the conformational flexibility of its structural scaffold. Here, we use a multistep strategy to investigate whether the same mechanism affects the functionality in the pepsin-like fold. (i) We identify the set of conserved residues by using sequence-alignment techniques. These residues cluster in three distinct regions: near the cleavage-site cavity, in the four beta-sheets cross-linking the two lobes, and in a solvent-exposed region below the long beta-hairpin in the N-terminal lobe. (ii) We elucidate the role played by the conserved residues for the enzymatic functionality of one representative member of the fold family, the human beta-secretase, by means of classical molecular dynamics (MD). The conserved regions exhibit little overall mobility and yet are involved into the most important modes of structural fluctuations. These modes influence the substrate-catalytic aspartates distance through a relative rotation of the N- and C-terminal lobes. (iii) We investigate the effects of this modulation by estimating the reaction free energy at different representative substrate/enzyme conformations. The activation free energy is strongly affected by large-scale protein motions, similarly to what has been observed in the HIV-1 enzyme. (iv) We extend our findings to all other members of the two eukaryotic and retroviral fold families by recurring to a simple, topology-based, energy functional. This analysis reveals a sophisticated mechanism of enzymatic activity modulation common to all aspartic proteases. We suggest that aspartic proteases have been evolutionarily selected to possess similar functional motions despite the observed fold variations.     

Synthesis of a ditopic cyclophane based on the cyclobutane ring by chalcone photocycloaddition

The intramolecular photocycloaddition of chalcones to give cyclobutanes has proven to be a fast and simple method to shrink a cyclophane ring to a tricyclic system, in order to prepare potential ditopic receptors. In particular, the chalcone 1, having dioxyethylene chains as spacers, is converted in high yield to the cyclobutane 2. NOESY spectroscopy indicates that the formation of 2 occurs by a head-to-head syn ring closure.     

ASV determination of cadmium complexation in seawater. Methodology evaluation

The methodology for using DPASV to study cadmium complexation in seawater is evaluated using EDTA as a model ligand and by analysing natural samples. The results show that the methodology gives an accurate evaluation of metal complexation when inert complexes are studied, both as regards the ligand concentration and the conditional stability constant; the error for both the parameters is lower than 10% at a ligand concentration of about 10(-8) M and a conditional stability constant of 10(9) M-1. Cadmium complexes with ligands present in natural seawater show an evident kinetic lability that may lead to underestimation of the conditional stability constant when a working electrode characterised by a very thick diffusion layer is used. The conditional stability constant in one water sample of the Adriatic coast ranged between 0.14 and 1.4 l/nmol using a rotating disk electrode at rotation rates of 300 and 6000 rpm. The results of cadmium complexation obtained for samples collected in coastal seawater show that the ligands present low specificity for the metal.     

Structural characterization techniques for the analysis of semiconductor strained heterostructures

A combined method for structural characterization of strained epitaxial heterostructures involving different techniques such as Rutherford backscattering spectrometry (RBS), multiple crystal X-ray diffractometry (MCD) and transmission electron microscopy (TEM) is presented. In order to obtain a complete characterization of the analysed structure, three different quantities are measured independently: the epilayer thickness, the density of misfit dislocations which may appear at the interface, and the significant components of the strain tensor, mainly the tetragonal distortion, affecting the epilayer lattice. In this way the thermodynamic state and the mechanisms of plastic deformation of the structures can be fully investigated. In this contribution we present and discuss the experimental results concerning a set of InP/GaAs samples having different layer thicknesses ranging from 5 to 500 nm. The thickness of the samples has been determined by RBS. Measurements of in-plane strain and tetragonal distortion have been performed by MCD and RBS-channelling respectively, finally TEM has been used for determining the defects densities and distribution.     

Volumetric Properties of Binary Mixtures of Isomeric Butanols and C8 Solvents at 298.15 K

Excess molar volumes, V _m ^E, over the whole composition range for binary mixtures of 1-butanol, 2-butanol, and 2-methyl-2-propanol + 1-octanol, or 2-octanol, or di-n-butyl ether, or n-hexylacetate were determined at 298.15 K from density measurements carried out with a vibrating-tube densimeter. Small V _m ^E values, both positive and negative, are displayed by mixtures containing 1- or 2-octanol, whereas positive and larger values are always found for mixtures containing dibutyl ether and hexylacetate. These results can be justified in terms of H-bonding interactions and/or steric hindrance due to the branched alkyl chains. Partial molar volumes at infinite dilution of the isomeric butanols in the C8 compounds were also calculated from the apparent molar volumes in dilute solution. The solute-solvent interactions and the effects of the local organisation of the solvent around the butanol molecules were discussed using the void and cavity volumes as different estimates of the intrinsic volume of the molecules. The volumetric behavior of butanols seems to be determined by the solute-solvent interactions rather than packaging effects.     

Transition metal-catalysed sequences of nucleophilic addition

Summary In presence of nickel or palladium catalysts, nucleophiles can attack vinylcyclopropanes with concomitant ring cleavage. With palladium catalysts in presence of appropriate substituents the terminal carbon atom of the resulting open chain is able to add to two molecules of a conjugated diene giving rise to long-chain unsaturated compounds.     

Self-assembly of electron donor-acceptor dyads into ordered architectures in two and three dimensions: surface patterning and columnar "double cables"

We report the synthesis and characterization of covalent dyads and multiads of electron acceptors (A) and donors (D), with the purpose of exploiting their nanophase separation behavior toward (a) two-dimensional (2D) surface patterning with well-defined integrated arrays of dissimilar molecular electronic features and (b) bulk self-assembly to noncovalent columnar versions of the so-called "double cable" systems, the likes of which could eventually provide side-by-side percolation pathways for electrons and holes in solar cells. Soluble, alkylated hexa-peri-hexabenzocoronenes (HBCs) bearing tethered anthraquinones (AQs) are shown by scanning tunneling microscopy (STM) to self-assemble at the solution-graphite interface into either defect-rich polycrystalline monolayers or extended 2D crystalline domains, depending on the number of tethered AQs. In the bulk, the thermal stability of the room-temperature HBC columnar phase is increased, which is attributed to the desired nanotriphase separation of HBC columns, insulating alkyl sheaths, and AQ units. Homeotropic alignment (columns normal to surfaces), predicted to be ideal for potential exploitation of such "double cables" in photovoltaic devices, is demonstrated.     

Standard pH values for potassium hydrogenphthalate reference buffer solutions in 10, 30 and 50% (w/w) 1,4-dioxane/water mixed solvents at temperatures from 288.15 to 318.15 K

Standard pH(S) values for 0.05 mol kg^?1 potassium hydrogenphthalate (KHpH) reference buffer solutions in 10, 30 and 50% (w/w) 1,4-dioxane/water solvent mixtures within the temperature range 288.15–318.15 K are determined from e.m.f. measurements of the cell without transference Pt|H₂|KHPh + KCl|AgCl|Ag|Pt. The consistency of the results is analysed by a recently described method of multilinear regression of the quantity p(a_Hγ_Cl) as a function of both solution composition and temperature. The standard pH(S) determined can be reproduced to within ±0.01 by the equation pH(S) - 4.004 + 3.309w + 0.408z + 1.037w³ - 14.95zw² + 27.1zw³, where w is the weight fraction of dioxane in the solvent mixture,z = (T –θ)/θ, and θ - 298.15 K. Values of the first ionization constant of phthalic acid (H₂Ph; benzene-1,2-dicarboxylic acid) in the above solvent mixtures are also determined from e.m.f. measurements of the cell without transference Pt|H₂|H₂Ph + KHPh + KCl|AgCl|Ag|Pt.     

Iodocyclization/base-induced hydrodeiodination reaction of 5-substituted 4-alkenols. The influence of substituent on the stereoselective pathway

The electrophilic iodocyclization reaction of (Z)- and (E)-5-n-alkylsubstituted 4-alken-1-ols followed by base-induced hydrodeiodination reaction stereoselectively gave, respectively, (Z)- and (E)-alkylidentetrahydrofurans in high yield. Completely different outcomes were observed with (Z)- and (E)-6,6-dimethylhept-4-en-1-ol: their iodocyclization furnished, respectively, threo- and erythro-2-(1-iodo-2,2-dimetylpropyl)tetrahydrofuran with high stereoselectivity. The threo isomer gave clean formation of 6-tert-butyl-3,4-dihydro-2H-pyran by base-induced ring expansion, while erythro isomer underwent a base-induced ring contraction to 1-cyclopropyl-3,3-dimethylbutan-1-one. Moreover, (Z)- and (E)-5-cyclopropylpent-4-en-1-ol underwent a 6-endo-iodocyclization to threo- and erythro-2-cyclopropyl-3-iodotetrahydro-2H-pyran, respectively, that under the same basic treatment, gave two isomeric 6-cyclopropyldihydro-2H-pyrans in a stereoselective fashion.     

Calculation of electric dipole hypershieldings at the nuclei in the Hellmann-Feynman approximation

The third-rank electric hypershieldings at the nuclei of four small molecules have been evaluated at the Hartree-Fock level of theory in the Hellmann-Feynman approximation. The nuclear electric hypershieldings are closely related to molecular vibrational absorption intensities and a generalization of the atomic polar tensors (expanded in powers of the electric field strength) is proposed to rationalize these intensities. It is shown that the sum rules for rototranslational invariance and the constraints imposed by the virial theorem provide useful criteria for basis-set completeness and for near Hartree-Fock quality of nuclear shieldings and hypershieldings evaluated in the Hellmann-Feynman approximation. Twelve basis sets of different size and quality have been employed for the water molecule in an extended numerical test on the practicality of the proposed scheme. The best results are obtained with the R12 and R12+ basis sets, designed for the calculation of electronic energies by the explicitly correlated R12 method. The R12 basis set is subsequently used to investigate three other molecules, CO, N2, and NH3, verifying that the R12 basis consistently performs very well.