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Dissociative and molecular water adsorption on the anatase (001) surface is studied in the context of state-of-the-art density functional theory in large supercells suited for adsorption studies at various water coverage ratios. At low coverage values below 1/4 ML, water adsorption remains dissociative and a network of hydrogen bonds between the so formed hydroxyl groups favors the formation of a ridge surface structure. The hydroxyl patterned (4 × 4) surface thus undergoes a (2 × 4) reconstruction that causes the relief of the large tensile stress measured in the unreconstructed surface along the direction orthogonal to the ridge. This phenomenology is accompanied by the loss of reactivity of the reconstructed surface with respect to the dissociative water adsorption that becomes molecular above 1/4 ML. We also show that the molecular adsorption on the terrace is weaker than the one on the ridge. The present water reconstruction model is discussed and compared to the well-known ADM model of the reconstru...

Supramolecular architectures involving DNA bases can have a strong impact in several fields such as nanomedicine and nanodevice manufacturing. To date, in addition to the four canonical nucleobases (adenine, thymine, guanine and cytosine), four other forms of cytosine modified at the 5 position have been identified in DNA. Among these four new cytosine derivatives, 5-carboxylcytosine has been recently discovered in mammalian stem cell DNA, and proposed as the final product of the oxidative epigenetic demethylation pathway on the 5 position of cytosine. In this work, a calcium salt of 5-carboxylcytosine has been synthesized and deposited on graphite surface, where it forms self-assembled features as long range monolayers and up to one micron long filaments. These structures have been analyzed in details combining different theoretical and experimental approaches: X-ray single-crystal diffraction data were used to simulate the molecule-graphite interaction, first using molecular dynamics and then refining the results using density functional theory (DFT); finally, data obtained with DFT were used to rationalize atomic force microscopy (AFM) results.

Damage formation is investigated in GaAs implanted with 1 MeV Si ions to ion fluences from $3\ifmmode\times\else\texttimes\fi{}{10}^{12}$ to $5\ifmmode\times\else\texttimes\fi{}{10}^{15}\phantom{\rule{4pt}{0ex}}{\mathrm{cm}}^{\ensuremath{-}2}$ at room temperature. Under the conditions applied, amorphization of the implanted layers does not occur. The weakly damaged layers are studied by applying different experimental techniques including Rutherford backscattering spectrometry in channeling configuration, x-ray diffraction, in situ curvature measurement, optical subgap spectroscopy, and transmission electron microscopy. The results are evaluated and quantitatively connected with each other. Damage formation is described as a function of the ion fluence using a common defect evolution model. Point defects and defect clusters have to be taken into account in the ion fluence range of main interest up to $2\ifmmode\times\else\texttimes\fi{}{10}^{15}\phantom{\rule{4pt}{0ex}}{\mathrm{cm}}^{\ensuremath{-}2}$. Point defects contribute by a factor of about 8 more to both perpendicular strain and in-plane stress than defect clusters. When the concentration of point defects or the induced strain reaches a critical value, defect clusters form, which ensures that no further increase of perpendicular strain occurs. This reveals a clear driving force for cluster formation. The microstructure of the defect clusters cannot be determined from the results. ${\mathrm{As}}_{3}{\mathrm{Ga}}_{2}$ interstitial clusters are supposed. A remarkable decrease of the shear modulus of the implanted layers below the value of pristine GaAs by $\ensuremath{\approx}\ensuremath{-}35%$ is observed. Surprisingly, the change of shear modulus already sets in at a very low damage level of a few percent.

Using first principles calculations based on density functional theory, the electronic, vibrational and superconducting properties of compounds with different stoichiometry ratios in the A15 phase have been studied. To this purpose, the λ mass enhancement parameter, which determines the superconducting critical temperature through the Allen-Dynes modification of the McMillan formula, has been explicitly calculated in the context of the density functional perturbation theory that allows the calculation of the matrix elements of the electron-phonon interactions at different compositions related to the Sn content. Our results provide a better understanding of the inhomogeneous composition of one of the most widely employed low-temperature superconductors, evidencing the electronic properties and the phonon modes that are responsible for the critical temperature degradation as the Sn concentration is varied. © the Owner Societies 2016.

Solid-state nanopores and nanogaps are emerging as promising tools for single molecule analysis. 2D materials, such as graphene, can potentially reach the spatial resolution needed for nucleic acid and protein sequencing. In the context of the density functional theory, atomistic modeling and non-equilibrium Green's function calculation, we show that glycine based polypeptide chains translocating across a nano-gap between two semi-infinite graphene nano-ribbons leave a specific transverse current signature for each peptide bond. The projected density of states and bond current analyses reveal a complex scenario with a role played by the adjacent α-carbons and side chains and by the orbitals of the partially resonant double bond involving C, N and O atoms of the peptide bond. In this context, specific fingerprints of the atoms involved in the peptide bonds are found. The same scenario is evidenced also for peptides involving alanine residues. The signal measured can be considered as a specific fingerprint of peptide bonds between small and neutral amino acids with no polar/charge effects. On this basis, a newly conceived nano-device made of a graphene based array of nano-gap is proposed as a possible route to approach peptide sequencing with atomic resolution.

We report on the investigations of the structural and superconducting properties of Nb3Sn in the GPa range by angular dispersive synchrotron X-ray diffraction and ab-initio calculations based on density functional theory. X-ray Diffraction experiments were carried out on Nb3Sn technological samples to explore the equation of state at room temperature and at pressures up to 43.5 GPa: We observe an anomaly in the P-V curve in the region 5-10 GPa. The ab-initio calculated lattice parameter of Nb3 Sn as a function of pressure has been used as an input for the calculation of the phonon dispersion curves and of the electronic band structures along different high-symmetry directions in the Brillouin zone. The critical temperature has been calculated as a function of the hydrostatic pressure by means of the Allen-Dynes modification of the McMillan formula: We found that its behavior is dictated mostly by the electronic contribution, but evident anomalies up to 6 GPa arise from phonons. These findings are a clue that Nb3 Sn could have some structural instabilities with impact on its superconducting properties when subjected to a pressure of a few GPa and they represent an important step to understand and optimize the performances of Nb3Sn materials under the hard operational conditions of high field superconducting magnets. © 2002-2011 IEEE.

First principles calculations based on density functional theory and many body perturbation theory have been employed to study the optical absorption properties of a newly synthesized oligo-thiophene molecule, with a quaterthiophene central unit, that has been designed for solution-processed bulk-heterojunction solar cells. To this aim we have employed the GW approach to obtain quasiparticle energies as a pre-requisite to solve the Bethe-Salpeter equation for the excitonic Hamiltonian. We show that the experimental absorption spectrum can be explained only by taking into account the inter-molecular transitions among the π-stacked poly-conjugated molecules that are typically obtained in solid-state organic samples.

(101) anatase TiO2 surface in water ambient is an important system for the interaction of biocompatible nanodevices with biological environment. Following the experimental evidence showing that water molecules are mobile at temperature as low as 190 K and tend to form clusters along the [111]/[111] surface directions, a complete theoretical characterization of the dynamical properties of the first water layer on the (101) anatase TiO2 surface is presented. A variety of computational techniques have been employed in the context of the transition-state theory in the harmonic regime, ranging from first-principles total energy ground-state calculations, to density functional perturbation theory, minimum energy path search, and kinetic Monte Carlo simulations, to explain the experimental results on water kinetics on the (101) anatase TiO2 surface. We have calculated the migration energy barrier of water molecules, the vibrational prefactor through the phonon density of states, and the hopping rate along two pr...

The interface of biological molecules with inorganic surfaces has been the subject of several recent studies. Experimentally some amino acids are evidenced to play a critical role in the adhesion and selectivity on oxide surfaces; however, detailed information on how the water molecules on the hydrated surface are able to mediate the adsorption is still missing. Accurate total energy ab initio calculations based on dispersion-corrected density functional theory have been performed to investigate the adsorption of selected amino acids on the hydrated ZnO(101¯0) surface, and the results are presented and discussed in this paper. We have also investigated the role played by water in the determination of the most energetically favorable adsorption configurations of the selected amino acids. We have found that for some amino acids the most energetically favorable configurations involve the deprotonation of the molecule if the water screening is not effective. © 2015 American Chemical Society.