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Ohmann R.,Max Planck Institute for Solid State Research | Levita G.,Max Planck Institute for Solid State Research | Levita G.,National Simulation Center | Vitali L.,Max Planck Institute for Solid State Research | And 5 more authors.
ACS Nano | Year: 2011

The asymmetric molecule 4-[trans-2-(pyrid-4-yl-vinyl)] benzoic acid (PVBA) adsorbed on Cu(111) is characterized by scanning tunneling microscopy (STM) and density functional theory (DFT) to determine the influence of subsurface atomic layers on the adsorption. In contrast to the 6-fold symmetry of the first atomic layer of close-packed surfaces, we find that the arrangement of the isolated molecules follows predominantly a 3-fold symmetry. This reduction in symmetry, where the molecule selects a specific orientation along the 〈-211〉 axes, reveals the contribution of lower-lying Cu layers to the molecular arrangement. Our calculations rationalize the interaction of the substrate with the molecule in terms of electrostatic screening and local relaxation phenomena. © 2011 American Chemical Society.

Longo G.S.,Northwestern University | Bhattacharya S.Kr.,Abdus Salam International Center For Theoretical Physics | Scandolo S.,Abdus Salam International Center For Theoretical Physics | Scandolo S.,National Simulation Center
Journal of Physical Chemistry C | Year: 2012

Starting from ab initio calculations and using a force matching procedure, we have developed a new force field for molecular dynamics simulations of self-assembled monolayers of methylthiolate (MT) on Au(111) surfaces. This new force field is able to reproduce several observed features of SAMs of MT on Au(111) surface, such as the formation of gold vacancy islands and the (√3 × √3)R30 lattice. We have studied the dynamics of Au adatoms and monatomic vacancies on the Au(111) surface for the SAM of MT at room temperature. It is observed that monatomic vacancies coarsen to form large vacancy islands while the adatoms group to form clusters. Both results are in agreement with experiments. At elevated temperatures, Au adatoms that are lifted from the surface leave an atomic vacancy on it. The liquid-like diffusion of gold adatoms on the SAM surface occurs by hopping between pairs of methylthiolate to which the adatom is temporarily bound. Our findings indicate that structural models of the c(4 × 2) unit cell including adatoms and vacancies at room temperature need to be revisited. © 2012 American Chemical Society.

Ambrosetti A.,University of Padua | Ambrosetti A.,National Simulation Center | Silvestrelli P.L.,University of Padua | Silvestrelli P.L.,National Simulation Center
Journal of Physical Chemistry C | Year: 2011

The recently developed, efficient DFT/vdW-WF method for the inclusion of the van der Waals interactions in density functional theory (DFT), based on the use of the maximally localized Wannier functions, is applied to the study of the adsorption of rare-gas atoms (He, Ar, and Xe) and a water molecule on graphite and graphene surfaces, at three high-symmetry sites, by evaluating the equilibrium binding energies and distances. The results, compared to previous theoretical calculations and experimental estimates, are promising, particularly considering that the method is free from system-dependent fitted parameters. The crucial role of the chosen reference DFT functional is discussed in detail, and possible strategies to improve the method and overcome some present limitations are proposed. © 2011 American Chemical Society.

Rossato L.,University of Padua | Rossato L.,National Simulation Center | Rossetto F.,University of Padua | Rossetto F.,National Simulation Center | And 2 more authors.
Journal of Physical Chemistry B | Year: 2012

Structural, dynamical, bonding, and electronic properties of water molecules around a soluted methane molecule are studied from first principles. The results are compatible with experiments and qualitatively support the conclusions of recent classical molecular dynamics simulations concerning the controversial issue on the presence of "immobilized" water molecules around hydrophobic groups: the hydrophobic solute slightly reduces (by a less than 2 factor) the mobility of many surrounding water molecules rather than immobilizing just the few ones which are closest to methane, similarly to what was obtained by previous first-principles simulations of soluted methanol. Moreover, the rotational slowing down is compatible with the one predicted on the basis of the excluded volume fraction, which leads to a slower hydrogen bond exchange rate. The analysis of simulations performed at different temperatures suggests that the target temperature of the soluted system must be carefully chosen, in order to avoid artificial slowing-down effects. By generating maximally localized Wannier functions, a detailed description of the polarization effects in both solute and solvent molecules is obtained, which better characterizes the solvation process. © 2012 American Chemical Society.

Ambrosetti A.,University of Padua | Ambrosetti A.,National Simulation Center | Silvestrelli P.L.,University of Padua | Silvestrelli P.L.,National Simulation Center
Journal of Physical Chemistry C | Year: 2014

Thanks to its single atom thickness and its mechanical strength, nanoporous graphene is currently being regarded as a promising candidate for efficient and reliable gas separation applications. Clearly, the accurate energetic characterization of the penetration processes involving relevant gas-phase molecules is a fundamental prerequisite for any possible application. Here we evaluate permeation barriers and adsorption energies of the H2O, CH4, CO, CO2, O2, and H2 molecules and of the Ar atom on two types of hydrogen saturated pores by means of ab initio simulations, based on the density functional theory (DFT), able to include dispersion corrections too. We find that, although the qualitative trend followed by the values of the permeation barriers of the considered molecules is independent of the adopted DFT functional, at a quantitative level the results are noticeably affected by the dispersion corrections and the chosen exchange contribution characterizing the different functionals, as well as by the allowed graphene sheet distortions. Interestingly, we observe that, due to the occurrence of nontrivial H-bond interactions with the pore-saturating H atoms, the permeation barrier of water remains low even considering a small-size pore. The barrier is further diminished when considering the interaction with a second water molecule on the opposite side of the pore. These observations, combined with the relatively strong binding of the water molecule with the defected surface, suggests that porous graphene could also represent a promising membrane for water filtration. © 2014 American Chemical Society.

Faussurier G.,CEA DAM Ile-de-France | Blancard C.,CEA DAM Ile-de-France | Silvestrelli P.L.,University of Padua | Silvestrelli P.L.,National Simulation Center
Physical Review B - Condensed Matter and Materials Physics | Year: 2010

We used a variational approach adapted to a quantum molecular-dynamics code to determine the best reference potential for warm dense aluminum. This ab initio variational approach was based on the Gibbs-Bogolyubov inequality. We used many-body reference systems interacting through inverse-power-law potentials, among which the Coulomb potential was a particular case defining the classical one-component plasma model. By comparisons with full quantum molecular-dynamics simulations, we found that the Coulomb potential was not always the best reference potential. We calculated the self-diffusion coefficient and the shear viscosity and discussed the results obtained using the Chisolm-Wallace relation in the warm dense matter regime. © 2010 The American Physical Society.

Ambrosetti A.,University of Padua | Ambrosetti A.,National Simulation Center | Silvestrelli P.L.,University of Padua | Silvestrelli P.L.,National Simulation Center
Physical Review B - Condensed Matter and Materials Physics | Year: 2012

A different implementation is proposed for including van der Waals interactions in density functional theory using the maximally localized Wannier functions. With respect to the previous DFT/vdW-WF method, the present DFT/vdW-WF2 approach, which is based on the simpler London expression and takes into account the intrafragment overlap of the localized Wannier functions, leads to a considerable improvement in the evaluation of the C 6 van der Waals coefficients, as shown by the application to a set of selected dimers. Preliminary results on Ar on graphite and Ne on the Cu(111) metal surface also suggest that the C 3 coefficients characterizing molecule-surfaces van der Waals interactions are better estimated with this scheme. © 2012 American Physical Society.

Costanzo F.,University of Bologna | Venuti E.,University of Bologna | Della Valle R.G.,University of Bologna | Brillante A.,University of Bologna | And 2 more authors.
Journal of Physical Chemistry C | Year: 2010

The nature of the interaction of a series of α-oligothiophenes (1T up to 6T) with a Si(001) surface was studied by means of density functional theory (DFT) structural optimizations. For 1T, we found that the products of the [4 + 2] cycloaddition are more thermodynamically stable than those of the [2 + 2] cycloaddition, in agreement with previous cluster approach calculations. Since there are many possible ways of placing the all-trans nT molecule on a Si(001) surface, we have tested a number of possible conformations; in particular, starting from simple geometric considerations, we built the 6T molecule from 1T as a result of [2 + 2] cycloadditions. The binding energy of oligomers with n from 2 to 6 displays a steady drop, attributable to an increased deformation energy. Our study sheds light on the chemisorption of oligothiophenes on Si(001) showing, in particular, that molecular chemisorption is possible for oligothiophenes with up to four thiophene units. For 6T, we estimated the van der Waals contribution to the binding energy, being of the order of 1 eV for molecule-surface distances , in agreement with the experimental evidence of the presence of 6T physisorbed states on the Si(111) surface. Finally, the calculated work function for 6T on Si(001) is in very good agreement with the experimental estimate. © 2010 American Chemical Society.

Ensing B.,University of Amsterdam | Costanzo F.,University of Padua | Silvestrelli P.L.,University of Padua | Silvestrelli P.L.,National Simulation Center
Journal of Physical Chemistry A | Year: 2012

Since the recent achievement of Kurotobi and Murata to capture a water molecule in a C60 fullerene (Science2011, 333, 613), there has been a debate about the properties of this H2O@C60 complex. In particular, the polarity of the complex, which is thought to be underlying the easy separation of H2O@C60 from the empty fullerene by HPLC, was calculated and found to be almost equal to that of an isolated water molecule. Here we present our detailed analysis of the charge distribution of the water-encapsulated C60 complex, which shows that the polarity of the complex is, with 0.5 ± 0.1 D, indeed substantial, but significantly smaller than that of H2O. This may have important implications for the aim to design water-soluble and biocompatible fullerenes. © 2012 American Chemical Society.

Piccini G.,Humboldt University of Berlin | Havenith R.W.A.,Zernike Institute for Advanced Materials | Broer R.,Zernike Institute for Advanced Materials | Stener M.,University of Trieste | And 2 more authors.
Journal of Physical Chemistry C | Year: 2013

The surface plasmon resonance has been theoretically investigated in gold nanowires by means of time-dependent density functional theory. Linear chains of Au atoms and nanowires with the structure of the fcc bulk gold grown along the (110) and (111) directions have been considered. The effects of changing the length and the section on the plasmon have been studied. Strong photoabsorption is found when the length is above 2 nm: in that case the absorption profile is characterized by a sharp peak, and its analysis reveals that many configurations contribute to the transition, confirming its collective nature as an s ← s intraband transition. As expected, the effect of increasing the length is reflected in a red shift of the plasmon. © 2013 American Chemical Society.

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