5 research outputs found

    Structural Behaviors of Cytosine into the Hydrated Interlayer of Na<sup>+</sup>‑Montmorillonite Clay. An ab Initio Molecular Dynamics Study

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    Structural behaviors of cytosine in the hydrated Na<sup>+</sup>-montmorillonite clay interlayer have been investigated via ab initio molecular dynamics simulations. Short constrained simulations have been carried out by increasing the distance between the nucleobase and the surface. Structural data shows that a three water layer structure is more or less maintained in the interlayer, depending on the orientation of the nucleobase. Close to the surface, the cytosine remains in a coplanar orientation, which is stabilized by dispersion forces between the π system of cytosine and the surface. The Na<sup>+</sup> cation is adsorbed on the surface and is coordinated to cytosine through the O2 heteroatom, more accessible than N3, the latter interacting with water. The water interlayer molecules interact with both the nucleobase heteroatoms and the adsorbed cation. However, when the nucleobase gets away from the surface, it adopts an almost orthogonal orientation and interacts with the surface oxygen atoms via hydrogen bonds between the C5 and the amino hydrogen atoms. The Na<sup>+</sup> cation becomes hydrated and coordinates to cytosine via both the N3 and O2 atoms. The profile of the forces between cytosine and the surface helped us to identify stable configurations of cytosine at different nucleobase–clay distances. Longer simulations for the observed stable configurations have shown that the nucleobase remains stacked over the surface up to a distance of 4.9 Å. At a larger distance cytosine engages hydrogen bonds with the surface, in a more or less defined orthogonal orientation

    () Electrostatic interaction energy (Δ) between cytosine and the substituted benzenes Ph-X (kcal/mol) versus the local hardness η()

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    <p><b>Copyright information:</b></p><p>Taken from "Influence of the π–π interaction on the hydrogen bonding capacity of stacked DNA/RNA bases"</p><p>Nucleic Acids Research 2005;33(6):1779-1789.</p><p>Published online 23 Mar 2005</p><p>PMCID:PMC1069514.</p><p>© The Author 2005. Published by Oxford University Press. All rights reserved</p> () Correlation part of the interaction energy (Δ) between cytosine and the substituted benzenes Ph-X (kcal/mol) versus the benzene ring polarizability divided by (see ) (a.u.)

    Η() can be used for the estimation of the electrostatic interaction and the hydrogen bonding ability

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    <p><b>Copyright information:</b></p><p>Taken from "Influence of the π–π interaction on the hydrogen bonding capacity of stacked DNA/RNA bases"</p><p>Nucleic Acids Research 2005;33(6):1779-1789.</p><p>Published online 23 Mar 2005</p><p>PMCID:PMC1069514.</p><p>© The Author 2005. Published by Oxford University Press. All rights reserved</p

    Correlation part of the interaction energy (Δ) computed for the 10 stacked DNA/RNA base dimers (kcal/mol) versus the product of the polarizabilities of each base over (see ) (a

    No full text
    <p><b>Copyright information:</b></p><p>Taken from "Influence of the π–π interaction on the hydrogen bonding capacity of stacked DNA/RNA bases"</p><p>Nucleic Acids Research 2005;33(6):1779-1789.</p><p>Published online 23 Mar 2005</p><p>PMCID:PMC1069514.</p><p>© The Author 2005. Published by Oxford University Press. All rights reserved</p>u.)

    Hydrogen-Induced Adsorption of Carbon Monoxide on the Gold Dimer Cation: A Joint Experimental and DFT Investigation

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    It is demonstrated, using tandem mass spectrometry and radio frequency ion trap, that the adsorption of a H atom on the gold dimer cation, Au<sub>2</sub>H<sup>+</sup>, prevents its dissociation and allows for adsorption of CO. Reaction kinetics are measured by employing a radio frequency ion trap, where Au<sub>2</sub><sup>+</sup> and CO interact for a given reaction time. The effect of a hydrogen atom is evaluated by comparing reaction rate constants measured for Au<sub>2</sub><sup>+</sup> and Au<sub>2</sub>H<sup>+</sup>. The theoretical results for the adsorption of CO molecules and their reaction characteristics with Au<sub>2</sub><sup>+</sup> and Au<sub>2</sub>H<sup>+</sup> are found to agree with the experimental findings. The joint investigations provide insights into hydrogen atom adsorption effects and consequent reaction mechanisms
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