DNA three-way junction with a dinuclear iron(II) supramolecular helicate at the center: a NMR structural study

A tetracationic supramolecular helicate, [Fe2L3]4+ (L = C25H20N4), with a triple-helical architecture is found to induce the formation of a three-way junction (3WJ) of deoxyribonucleotides with the helicate located in the center of the junction. NMR spectroscopic studies of the interaction between the M enantiomer of the helicate and two different oligonucleotides, [5'-d(TATGGTACCATA)]2 and [5'-d(CGTACG)]2, show that, in each case, the 2-fold symmetry of the helicate is lifted, while the 3-fold symmetry around the helicate axis is retained. The 1:3 helicate/DNA stoichiometry estimated from 1D NMR spectra supports a molecular model of a three-way junction composed of three strands. Three separate double-helical arms of the three-way junction are chemically identical giving rise to one set of proton resonances. The NOE contacts between the helicate and DNA unambiguously show that the helicate is fitted into the center of the three-way junction experiencing a hydrophobic 3-fold symmetric environment. Close stacking interactions between the ligand phenyl groups and the nucleotide bases are demonstrated through unusually large downfield shifts (1-2 ppm) of the phenyl protons. The unprecedented 3WJ arrangement observed in solution has also been found to exist in the crystal structure of the helicate adduct of [d(CGTACG)2] (Angew. Chem., Int. Ed. 2006, 45, 1227).     

TiO2-based photocatalysts impregnated with metallo-porphyrins employed for degradation of 4-nitrophenol in aqueous solutions: role of metal and macrocycle

Photodegradation of organic compounds in water solutions by means of economically advantageous and environment-friendly processes is a topic of growing interest. In recent years a great attention has been devoted to TiO₂-based photocatalysts for the oxidative degradation of various organic pollutants. In this context, we have prepared new photo-catalytic polycrystalline TiO₂ systems impregnated with sensitizers, i.e., copper, iron or manganese porphyrins, and investigated their photoactivity for 4-nitrophenol oxidation compared with that of bare TiO₂. A significant improvement of the photoreactivity was observed in the case of TiO₂ impregnated with copper porphyrin, while only a slight beneficial effect was observed in the case of iron porphyrin. In contrast, the presence of manganese porphyrin appeared to be detrimental.     

Self-Assembling of cytosine nucleoside into triply-bound dimers in acid Media. A comprehensive evaluation of proton-bound pyrimidine nucleosides by electrospray tandem mass spectrometry,X-rays diffractometry,and theoretical calculations

Electrospray tandem mass spectrometry (ESI-MS/MS) is used to evaluate the assembling of cytosine and thymine nucleosides in the gas phase, through the formation of hydrogen bonded supermolecules. Mixtures of cytidine analogues and homologues deliver in the gas phase proton-bound heterodimers stabilized by multiple interactions, as proven by the kinetics of their dissociation into the corresponding protonated monomers. Theoretical calculations, performed on initial structures of methylcytosine homodimers available in the literature, converged to a minimized structure whereby the two pyrimidine rings interact through the formation of three hydrogen bonds of similar energy. The crystallographic data here reported show the equivalency of the two interacting pyrimidines which is attributable to the presence of an inversion center. Thymine and uracil pyrimidyl nucleosides form, by ESI, gaseous proton-bound dimers. The kinetic of their dissociation into the related protonated monomers shows that the nucleobases are weekly interacting through a single hydrogen bond. The minimized structure of the protonated heterodimer formed by thymine and N-1-methylthymine confirmed the existence of mainly one hydrogen bond which links the two nucleobases through the O4 oxygens. No crystallographic data exists on thymine proton-bound species, nor have we been able to obtain these aggregates in the solid phase. The gaseous phase, under high vacuum conditions, seems therefore a suitable environment where vanishing structures produced by ESI can be studied with a good degree of approximation.     

Electrochemical Behavior of a Glassy Carbon Electrode Chemically Modified with Nickel Pentacyanonitrosylferrate in Presence of Sulfur Compounds

The glassy carbon electrode was modified with a nickel pentacyanonitrosylferrate film by electrodeposition of Ni and subsequent derivatization with NaPCNF. The film was characterized by XPS and electrochemical methods. Cyclic voltammetry of the NiPCNF onto the GC shows a redox couple (Fe^III/Fe^II) with E°′ of 538 mV (I_pa/I_pc around 1) and ΔE_p of 93 mV in 0.5 mol L^?1 KNO₃, with a diffusion‐controlled process. There was a decrease of anodic peak currents of the film in the presence of sulfide and 2‐propanethiol due to a precipitation reaction on the film surface by nucleophilic attack.     

Physical and morphological characteristics and electrochemical behaviour in PEM fuel cells of PtRu /C catalysts

Platinum-ruthenium catalysts supported on carbon (PtRu/C) have been characterized by X-ray diffraction (XRD), transmission electron microscopy (TEM), specific surface area analysis (BET), X-ray photoelectron spectroscopy (XPS) and in proton exchange membrane (PEM) fuel cell tests. The results indicate the presence of strong metal-carbon interactions, which hinder the formation of a single-phase face-centered cubic (fcc) PtRu alloy. The particle size of the PtRu/C catalysts was smaller than both carbon-supported platinum (Pt/C) and ruthenium (Ru/C) catalysts. In the bimetallic electrocatalysts the intercrystallite distance decreased with respect to pure Pt and Ru metals. PEM fuel cell tests in H₂/air operation mode revealed a decrease of performance with increasing carbon content of the catalyst, at a fixed Pt loading. In H₂ + 100 ppm CO/air operation mode the maximum performance of the PEM fuel cell was attained at 0.63 atomic fraction Ru. Received: 2 December 1999 / Accepted: 27 January 2000     

HTMoL: full-stack solution for remote access,visualization, and analysis of molecular dynamics trajectory data

Research on biology has seen significant advances with the use of molecular dynamics (MD) simulations. The MD methodology enables explanation and discovery of molecular mechanisms in a wide range of natural processes and biological systems. The need to readily share the ever-increasing amount of MD data has been hindered by the lack of specialized bioinformatic tools. The difficulty lies in the efficient management of the data, i.e., in sending and processing 3D information for its visualization. In this work, we present HTMoL, a plug-in-free, secure GPU-accelerated web application specifically designed to stream and visualize MD trajectory data on a web browser. Now, individual research labs can publish MD data on the Internet, or use HTMoL to profoundly improve scientific reports by including supplemental MD data in a journal publication. HTMoL can also be used as a visualization interface to access MD trajectories generated on a high-performance computer center directly. Furthermore, the HTMoL architecture can be leveraged with educational efforts to improve learning in the fields of biology, chemistry, and physics.     

On the influence of fatty acid chain unsaturation on supramolecular gelation of aminocarbohydrate-based supra-amphiphiles

Supramolecular gels are soft materials formed mainly by low molecular weight units held together by intermolecular interactions. Stabilizing these kinds of materials is quite a challenge due to the influence of multiple factors interfering with the integrity of the supramolecular structure. In our previous studies, we have shown that the aminocarbohydrate meglumine (MEG) interacts with organic acids by ion-pairing leading to the formation of MEG–carboxylate adducts. These adducts undergo supramolecular polymerization by heat treatment, but the macromolecular assembly was stable for a short period due to hydrogen bond (H-bond) breakup. Herein, we attempt to study the influence of hydrophobic building blocks on the formation of these compounds aiming to stabilize H-bonds to produce polymerizable supra-amphiphiles in water. Oleic acid and stearic acid are two analogous fatty acids differing only in the presence of unsaturation that were used in our studies. Results demonstrated that the presence of unsaturation hinders gelation in water by interfering with the self-assembly behavior of supra-amphiphiles. Thus, unsaturated supra-amphiphiles behave like traditional surfactants and gelify water at high concentrations (above 30% w/w). On the other hand, supramolecular gels with a polymer-like behavior could be produced with a saturated supra-amphiphile in water (above 4% w/w). The material was characterized by a lamellar arrangement that facilitates the alignment of H-bonds necessary to stabilize the self-assembled structure. These results have pivotal importance on the design of polymerizable supra-amphiphiles and demonstrate that the double bond of hydrophobic building blocks is an important design factor to be considered by scientists studying similar materials.     

Electron density fitting for the Coulomb problem in relativistic density-functional theory

A density fitting approach for the Coulomb matrix representation within the four-component formulation of relativistic density-functional theory is presented. Our implementation, which uses G-spinor basis sets, shares all the advantages of those found in nonrelativistic quantum chemistry. We show that very accurate Coulomb energies may be obtained using a modest number of scalar auxiliary basis functions for molecules containing heavy atoms. The efficiency of this new implementation is demonstrated in a detailed study of the spectroscopic properties of the gold dimer, and its scaling behavior has been tested by calculations of some closed-shell gold clusters (Au2, Au3+, Au4, Au5+). The algorithm is found to scale as O(N3), just as it does in the nonrelativistic case, and represents a dramatic improvement in efficiency over the conventional approach in the calculation of the Coulomb matrix, with computation times that are reduced to less than 3% for Au2 and up to 1% in the case of Au5+.