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Biomedical subjects

Angelo Bongiorno

Publications and source records attributed to Angelo Bongiorno.

9 recordsLinked to original sources
PubMed2006

Oxidative damage to DNA: counterion-assisted addition of water to ionized DNA.

Oxidative damage to DNA, implicated in mutagenesis, aging, and cancer, follows electron loss that generates a radical cation that migrates to a guanine, where it may react with water to form 8-oxo-7,8-dihydroguanine (8-OxoG). Molecular dynamics and ab initio quantum simulations on a B-DNA tetradecamer reveal activated reaction pathways that depend on the local counterion arrangement. The lowest activation barrier, 0.73 eV, is found for a reaction that starts from a configuration where a Na(+) resides in the major groove near the N7 atoms of adjacent guanines, and evolves through a transition state where a bond between a water oxygen atom and a carbon atom forms concurrently with displacement of a proton toward a neighboring water molecule. Subsequently, a bonded complex of a hydronium ion and the nearest backbone phosphate group forms. This counterion-assisted proton shuttle mechanism is supported by experiments exploiting selective substitution of backbone phosphates by methylphosphonates.

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PubMed2006

Bonding trends and dimensionality crossover of gold nanoclusters on metal-supported MgO thin films.

Bonding of gold clusters, , 16, and 20, on MgO(100) and on thin MgO films supported on Mo(100) is investigated using first-principles density-functional theory. Enhanced adhesive bonding is found for clusters deposited on metal-supported MgO films of thickness up to about 1 nm, or 4 to 5 MgO layers, originating from electrostatic interaction between the underlying metal and metal-induced excess electronic charge accumulated at the cluster interface with the oxide film. The increased wetting propensity is accompanied by a dimensionality crossover from three-dimensional optimal cluster geometries on MgO(100) to energetically favored two-dimensional structures on the metal-supported films.

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PubMed2005

Water-enhanced catalysis of CO oxidation on free and supported gold nanoclusters.

The enhancement by water molecules of the catalytic activity of gas-phase and supported gold nanoclusters toward CO oxidation is investigated with first-principles calculations. Coadsorption of H(2)O and O(2) leads to formation of a complex well bound to the gold cluster, even on a defect-free MgO(100) support. Formation of the complex involves partial proton sharing between the adsorbates, that in certain configurations results in proton transfer leading to the appearance of a hydroperoxyl-like complex. The O-O bond is activated, leading to a weakened peroxo or superoxolike state, and consequently the reaction with CO to form CO2 occurs with a small activation barrier of approximately 0.5 eV. A complete catalytic cycle of the water-enhanced CO oxidation is discussed.

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PubMed2004

Modeling phase separation in nonstoichiometric silica.

We have modeled the decomposition of nonstoichiometric amorphous SiOx upon annealing into silicon and stoichiometric silica, using a new method based on mapping Metropolis Monte Carlo simulations onto rate equations. The concentrations of all oxidation states of silicon are derived as a function of time and found to attain steady-state values at long times dependent on temperature T and oxygen content x. The degree of phase separation and the sizes of Si particles are predicted as a function of T and x, enabling greater control over the size of silicon quantum dots in silica matrices.

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PubMed2004

Reaction of the oxygen molecule at the Si(100)-SiO2 interface during silicon oxidation.

Using constrained ab initio molecular dynamics, we investigate the reaction of the O2 molecule at the Si(100)-SiO2 interface during Si oxidation. The reaction proceeds sequentially through the incorporation of the O2 molecule in a Si-Si bond and the dissociation of the resulting network O2 species. The oxidation reaction occurs nearly spontaneously and is exothermic, irrespective of the O2 spin state or of the amount of excess negative charge available at the interface. The reaction evolves through the generation of network coordination defects associated with charge transfers. Our investigation suggests that the Si oxidation process is fully governed by diffusion.

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PubMed2003

Transition structure at the Si(100)-SiO2 interface.

We characterize the transition structure at the Si(100)-SiO2 interface by addressing the inverse ion-scattering problem. We achieve sensitivity to Si displacements at the interface by carrying out ion-scattering measurements in the channeling geometry for varying ion energies. To interpret our experimental results, we generate realistic atomic-scale models using a first-principles approach and carry out ion-scattering simulations based on classical interatomic potentials. Silicon displacements larger than 0.09 A are found to propagate for three layers into the Si substrate, ruling out a transition structure with regularly ordered O bridges, as recently proposed.

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PubMed2002

Dielectric constants of Zr silicates: a first-principles study.

Using density-functional theory, we compute the optical and static dielectric constants for a set of Zr silicates modeled by various SiO2 crystals, with Zr atoms substitutional to Si, and by an amorphous structure. We then derive a microscopic scheme that relates the dielectric constants to structural units centered on Si and Zr atoms through the definition of characteristic parameters. Applied to amorphous (ZrO2)(x)(SiO2)(1-x), these schemes describe the observed dependence of the dielectric constants on the Zr concentration and highlight the role of ZrO6 units.

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PubMed2002

Oxygen diffusion through the disordered oxide network during silicon oxidation.

An atomic-scale description is provided for the long-range oxygen migration through the disordered SiO2 oxide during silicon oxidation. First-principles calculations, classical molecular dynamics, and Monte Carlo simulations are used in sequence to span the relevant length and time scales. The O2 molecule is firmly identified as the transported oxygen species and is found to percolate through interstices without exchanging oxygen atoms with the network. The interstitial network for O2 diffusion is statistically described in terms of its potential energy landscape and connectivity. The associated activation energy is found in agreement with experimental values.

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