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Simone S Alexandre

Publications and source records attributed to Simone S Alexandre.

6 recordsLinked to original sources
PubMed2006

Assembling of dimeric entities of Cd(II) with 6-mercaptopurine to afford one-dimensional coordination polymers: synthesis and scanning probe microscopy characterization.

The direct reaction between 6-mercaptopurine (6-MP) and Cd(II) under different conditions yields either [Cd2(6-MP)4(NO3)2](NO3)2 (1) or [Cd(6-MP-)2.2H2O]n (4). Compound 1 behaves as the building block of the polymer [Cd(6-MP2-)2]n[Ca(H2O)6]n (3), by deprotonation of 6-MP ligand. In the reaction of 1 to give 3, the dinuclear compound [Cd2(6-MP)4(H2O)2](NO3)4.2H2O (2) can be isolated as an intermediate. Polymers 3 and 4 convert into each other in water via deprotonation-protonation reactions. The structures of compounds 1-3 have been determined by X-ray diffraction. Given the small differences in the arrangement shown in the crystal structures of the polymer 4 and the polyanion of 3, the stabilities and energetics of the two arrangements have been examined by DFT calculations to determine the possibility of identifying new conformations of both polymers. In addition, the two polymers have been characterized on surfaces by means of AFM. The direct reaction between 6-MP and Cd(II) and the deprotonation of the polymer 4 have proven to be useful routes for the isolation of one-dimensional systems on surfaces. The development of new strategies to characterize these types of polymers on surfaces opens the possibility to perform nanoscale studies on their properties and their potential use as nanomaterials.

Journal Article↗
PubMed2005

Strain-dependence of the electronic properties in periodic quadruple helical G4-wires.

The electronic structure of periodic quadruple helix guanine wires, which mimic G4-DNA molecules, was studied as a function of the stacking distance between consecutive planes, by means of first principles density functional theory calculations. We show that, whereas for the native DNA interplane separation of 3.4 A the HOMO- and LUMO-derived bands are poorly dispersive, the bandwidths can be significantly increased when compressive strain is applied along the helical axis. Our findings indicate that efficient band conduction for both holes and electrons can be supported by such wires for stacking distances below 2.6 A, which imply a huge axial deformation with respect to double and quadruple helices in solutions and in crystals.

Computer Simulation↗
PubMed2005

Stabilization of the non-canonical adenine-adeninium base pair by N(7) coordination of Zn(II).

A new zinc (II) compound with 9-ethyladenine (9-EtA) of formula [Zn(9-EtA-N7)Cl(3)](9-EtAH) has been synthesized and characterized by X-ray diffraction. Its X-structure consists of an Zn(II) anionic complex and 9-ethyladeninium as counteranion. The Zn(II) complex shows a distorted tetrahedral geometry in which three Cl and an 9-EtA coordinates through N(7) position are the ligands. An indirect chelation via intramolecular H-bond between N(6)H and an Cl ligand is present in the complex. The network of [Zn(9-EtA-N7)Cl(3)](9-EtAH) shows interesting features. Thus, self-association of coordinated adenine-adeninium takes place by H-bonding of N(6)-H...N(1) and N(6)-H...N(7), leading to a polymeric ribbon-like 1D supramolecular arrangement. Ab initio calculations have been applied in order to study the stability of the adenine-adeninium interaction due to the coordination of the Zn(II) to the N(7) position and to compare experimental and theoretical structural data.

Adenine↗
PubMed2005

Structural models for the interaction of Cd(II) with DNA: trans-[Cd(9-RGH-N7)2(H2O)4]2+.

Reactions of Cd(NO(3))(2) with the model nucleobases 9-alkylguanine in water at neutral pH, give the compounds trans-[Cd(9-RGH-N7)(2)(H(2)O)(4)](NO(3))(2)(R=Me, Et), with the 9-alkylguanine ligands bound to the metal cation at the N(7) position. The X-ray structures of both compounds are reported. The six-coordinate Cd(II) complexes consist of a highly regular octahedral geometry in which the two 9-alkylguanine ligands are in a trans position to each other and approximately collinear with the metal cation. In addition, the networks of both compounds show interesting features. Thus, intramolecular H-bonds between O(6) and a coordinated water molecule are present, and self-association of guanines via H-bonding of N(3)-H...N(2) take place, leading to a 1D supramolecular polymeric ribbon. Density functional theory calculations have been applied to both compounds in order to study the stability of N(7) metalated guanine-guanine associations by comparing experimental and theoretical results. The potential relevance with regard to possible Cd(II)-DNA cross-links is briefly discussed.

Cadmium Compounds↗
PubMed2003

Small polarons in dry DNA.

We report ab initio calculations for positively charged fragments of dry poly(dC)-poly(dG) DNA, with up to 4 C-G pairs. We find a strong hole-lattice coupling and clear evidence for the formation of small polarons. The largest geometry distortions occur in only one or two base pairs. They involve the stretching of weak bonds within each base pair, increasing the distance of positive hydrogens, and decreasing that of negative oxygens, to the region in which the hole localizes. We obtain an energy of approximately 0.30 eV for the polaron formation, nearly independent of the chain size. From it, we can estimate an activation energy for polaron hopping of approximately 0.15 eV, consistent with the available experimental value.

Base Pairing↗