Nucleation of Pd dimers at defect sites of the MgO(100) surface

Point defects on oxide surfaces are presumed to be preferential nucleation sites for supported metal clusters. Under typical growth conditions, dimers constitute the first step in island nucleation. First-principles calculations on the formation of Pd dimers on regular and defect sites of the MgO(100) surface show that nucleation occurs with large dimer binding energies at divacancies and charged oxygen vacancies (F+ centers), while it is less favorable on steps and neutral F centers. The extensive database of defect trapping/attachment properties gives a firm basis to rationalize recent atomic-force microscopy findings and provides guidelines valid, in general, for ionic substrates.

Modeling H-bonding and solvent effects in the alkylation of pyrimidine bases by a prototype quinone methide: a DFT study

Nucleophilicity of NH(2), N3, and O(2) centers of cytosine toward a model quinone methide (o-QM) as alkylating agent has been studied using DFT computational analysis [at the B3LYP/6-311+G(d,p) level]. Specific and bulk effects of water (by C-PCM model) on the alkylation pathways have been evaluated by analyzing both unassisted and water-assisted reaction mechanisms. An ancillary water molecule, H-bonded to the alkylating agent, may interact monofunctionally with the o-QM oxygen atom (passive mechanisms) or may participate bifunctionally in cyclic hydrogen-bonded structures as a proton shuttle (active mechanisms). A comparison of the unassisted with the water-assisted reaction mechanisms has been made on the basis of activation Gibbs free energies (DeltaG(++)). The gas-phase alkylation reaction at N3 does proceed through a passive mechanism that is preferred over both the active (by -6.3 kcal mol(-1)) and the unassisted process. In contrast, in the gas phase, the active assisted processes at NH(2) and O(2) centers are both favored over their unassisted counterparts by -4.0 and -2.2 kcal mol(-1), respectively. The catalytic effect of a water molecule, in gas phase, reduces the gap between the TSs of the O(2) and NH(2) reaction pathways, but the former remains more stable. Water bulk effect significantly modifies the relative importance of the unassisted and water-assisted alkylation mechanisms, favoring the former, in comparison to the gas-phase reactions. In particular, the unassisted alkylation becomes the preferred mechanism for the reaction at both the exocyclic (NH(2)) and the heterocyclic (N3) nitrogen atoms. By contrast, alkylation at the cytosine oxygen atom is a water-catalyzed process, since in water the active water-assisted mechanism is still favored. As far as competition, among all the possible mechanisms, our calculations unambiguously suggest that the most nucleophilic site both in gas phase (naked reagents: N3 >> O(2) >or= NH(2)) and in water solution (solvated reagents: N3 >> NH(2) >> O(2)) is the heterocyclic nitrogen atom (N3) (DeltaG(++)(gas) = +7.1 kcal mol(-1), and DeltaG(++)(solv) = +13.7 kcal mol(-1)). Our investigation explains the high reactivity and selectivity of the cytosine moiety toward o-QM-like structures both in deoxymononucleoside and in a single-stranded DNA, on the basis of strong H-bonding interactions between reactants and solvent bulk effect. It also offers two general reactivity models in water, uncatalyzed and active water-catalyzed mechanisms (for nitrogen and oxygen nucleophiles, respectively), which should provide a general tool for the planning of nucleic acid modification.

Paramagnetic defect centers at the MgO surface. An alternative model to oxygen vacancies

On the basis of embedded cluster calculations, we propose a new model for the structure of paramagnetic color centers at the MgO surface usually denoted as F(S)(H)(+) (an electron trapped near an adsorbed proton). These centers are produced by exposing the surface of polycrystalline MgO to H(2) followed by UV irradiation. We demonstrate that properties of H atom absorbed at surface sites such as step edges (MgO(step)) and reverse corner sites (MgO(RC)), formed at the intersection of two step edges, are compatible with a number of features observed for F(S)(H)(+). Our calculations suggest that (i) H(2) dissociates at the reverse corner site heterolytically and that there is no barrier for this exothermic reaction; (ii) the calculated vibrations of the resulting MgO(RC)(H(+))(H(-)) complex are fully consistent with the measured ones; (iii) desorption of a neutral H atom from the diamagnetic precursor requires UV light and leads to the formation of stable neutral paramagnetic centers at the surface, MgO(step)(H(+))(e(-))(trapped) and MgO(RC)(H(+))(e(-))(trapped). The computed isotropic hyperfine coupling constants and optical transitions of these centers are in broad agreement with the existing experimental data. We argue that these centers, which do not belong to the class of "oxygen vacancies", are two of the many possible forms of the F(S)(H)(+) defect center.