MMonCa: A flexible and powerful new Kinetic Monte Carlo simulator

Kinetic Monte Carlo (KMC) is a widely used technique to simulate the evolution of radiation damage inside solids. Despite de fact that this technique was developed several decades ago, there is not an established and easy to access simulating tool for researchers interested in this field, unlike in the case of molecular dynamics or density functional theory calculations. In fact, scientists must develop their own tools or use unmaintained ones in order to perform these types of simulations. To fulfil this need, we have developed MMonCa, the Modular Monte Carlo simulator. MMonCa has been developed using professional C++ programming techniques and has been built on top of an interpreted language to allow having a powerful yet flexible, robust but customizable and easy to access modern simulator. Both non lattice and Lattice KMC modules have been developed. We will present in this conference, for the first time, the MMonCa simulator. Along with other (more detailed) contributions in this meeting, the versatility of MMonCa to study a number of problems in different materials (particularly, Fe and W) subject to a wide range of conditions will be shown. Regarding KMC simulations, we have studied neutron-generated cascade evolution in Fe (as a model material). Starting with a Frenkel pair distribution we have followed the defect evolution up to 450 K. Comparison with previous simulations and experiments shows excellent agreement. Furthermore, we have studied a more complex system (He-irradiated W:C) using a previous parametrization [1]. He-irradiation at 4 K followed by isochronal annealing steps up to 500 K has been simulated with MMonCa. The He energy was 400 eV or 3 keV. In the first case, no damage is associated to the He implantation, whereas in the second one, a significant Frenkel pair concentration (evolving into complex clusters) is associated to the He ions. We have been able to explain He desorption both in the absence and in the presence of Frenkel pairs and we have also applied MMonCa to high He doses and fluxes at elevated temperatures. He migration and trapping dominate the kinetics of He desorption. These processes will be discussed and compared to experimental results. [1] C.S. Becquart et al. J. Nucl. Mater. 403 (2010) 75

On the acidity and reactivity of HNO in aqueous solution and biological systems

The gas phase and aqueous thermochemistry and reactivity of nitroxyl (nitrosyl hydride, HNO) were elucidated with multiconfigurational self-consistent field and hybrid density functional theory calculations and continuum solvation methods. The pKa of HNO is predicted to be 7.2 ± 1.0, considerably different from the value of 4.7 reported from pulse radiolysis experiments. The ground-state triplet nature of NO− affects the rates of acid-base chemistry of the HNO/NO− couple. HNO is highly reactive toward dimerization and addition of soft nucleophiles but is predicted to undergo negligible hydration (Keq = 6.9 × 10−5). HNO is predicted to exist as a discrete species in solution and is a viable participant in the chemical biology of nitric oxide and derivatives.

Stretching dependence of the vibration modes of a single-molecule Pt-H2-Pt bridge

A conducting bridge of a single hydrogen molecule between Pt electrodes is formed in a break junction experiment. It has a conductance near the quantum unit, G0=2e2∕h, carried by a single channel. Using point-contact spectroscopy three vibration modes are observed and their variation upon isotope substitution is obtained. The stretching dependence for each of the modes allows uniquely classifying them as longitudinal or transversal modes. The interpretation of the experiment in terms of a Pt-H2-Pt bridge is verified by density-functional theory calculations for the stability, vibrational modes, and conductance of the structure.

Hydrogenated graphene nanoribbons for spintronics

We show how hydrogenation of graphene nanoribbons at small concentrations can open venues toward carbon-based spintronics applications regardless of any specific edge termination or passivation of the nanoribbons. Density-functional theory calculations show that an adsorbed H atom induces a spin density on the surrounding π orbitals whose symmetry and degree of localization depends on the distance to the edges of the nanoribbon. As expected for graphene-based systems, these induced magnetic moments interact ferromagnetically or antiferromagnetically depending on the relative adsorption graphene sublattice, but the magnitude of the interactions are found to strongly vary with the position of the H atoms relative to the edges. We also calculate, with the help of the Hubbard model, the transport properties of hydrogenated armchair semiconducting graphene nanoribbons in the diluted regime and show how the exchange coupling between H atoms can be exploited in the design of novel magnetoresistive devices.

Isoprene-mediated lithiation of imidazole derivatives: mechanism considerations

The isoprene-mediated lithiation, with lithium metal, of different imidazole derivatives is an interesting methodology for their functionalization. Studies of different possible intermediates involved in the reaction employing density functional theory calculations, at the B3LYP/6-311++G(d,p) level are considered. A plausible mechanism is described, in which isoprene is reduced, to the corresponding radical anion, in the presence of Li(s), acting then as a base deprotonating N-methylimidazole (NMI) and producing the 1,1-dimethylallyl radical. This radical is further reduced by the excess of lithium proceeding once more as a base. This final step produces stable final products that compensate the previous equilibriums, making favourable the whole process.

Mg-based nanocomposites with high capacity and fast kinetics for hydrogen storage

Magnesium and its alloys have shown a great potential in effective hydrogen storage due to their advantages of high volumetric/ gravimetric hydrogen storage capacity and low cost. However, the use of these materials in fuel cells for automotive applications at the present time is limited by high hydrogenation temperature and sluggish sorption kinetics. This paper presents the recent results of design and development of magnesium-based nanocomposites demonstrating the catalytic effects of carbon nanotubes and transition metals on hydrogen adsorption in these materials. The results are promising for the application of magnesium materials for hydrogen storage, with significantly reduced absorption temperatures and enhanced ab/desorption kinetics. High level Density Functional Theory calculations support the analysis of the hydrogenation mechanisms by revealing the detailed atomic and molecular interactions that underpin the catalytic roles of incorporated carbon and titanium, providing clear guidance for further design and development of such materials with better hydrogen storage properties.

Chemical and structural disorder in eumelanins: A possible explanation for broadband absorbance

We report the results of an experimental and theoretical study of the electronic and structural properties of a key eumelanin precursor-5,6,-dihydroxyindole-2-carboxylic acid ( DHICA) - and its dimeric forms. We have used optical spectroscopy to follow the oxidative polymerization of DHICA to eumelanin and observe red shifting and broadening of the absorption spectrum as the reaction proceeds. First principles density functional theory calculations indicate that DHICA oligomers ( possible reaction products of oxidative polymerization) have the gap between the highest occupied molecular orbital and the lowest unoccupied molecular orbital red-shifted gaps with respect to the monomer. Furthermore, different bonding configurations ( leading to oligomers with different structures) produce a range of gaps. These experimental and theoretical results lend support to the chemical disorder model where the broadband monotonic absorption characteristic of all melanins is a consequence of the superposition of a large number of nonhomogeneously broadened Gaussian transitions associated with each of the components of a melanin ensemble. These results suggest that the traditional model of eumelanin as an amorphous organic semiconductor is not required to explain its optical properties and should be thoroughly reexamined. These results have significant implications for our understanding of the physics, chemistry, and biological function of these important biological macromolecules. Indeed, one may speculate that the robust functionality of melanins in vitro is a direct consequence of its heterogeneity, i.e., chemical disorder is a "low cost" natural resource in these systems

Synthetic, crystallographic, and computational study of copper(II) complexes of ethylenediaminetetracarboxylate ligands

Copper(II) complexes of hexadentate ethylenediaminetetracarboxylic acid type ligands Heda3p and Heddadp (Heda3p = ethylenediamine-N-acetic-N,N',N'-tri-3-propionic acid; H eddadp = ethylenediamine-N,N'-diacetic-N,N'-di-3- propionic acid) have been prepared. An octahedral trans(O) geometry (two propionate ligands coordinated in axial positions) has been established crystallographically for the Ba[Cu(eda3p)]·8HO compound, while Ba[Cu(eddadp)]·8HO is proposed to adopt a trans(O ) geometry (two axial acetates) on the basis of density functional theory calculations and comparisons of IR and UV-vis spectral data. Experimental and computed structural data correlating similar copper(II) chelate complexes have been used to better understand the isomerism and departure from regular octahedral geometry within the series. The in-plane O-Cu-N chelate angles show the smallest deviation from the ideal octahedral value of 90°, and hence the lowest strain, for the eddadp complex with two equatorial ß-propionate rings. A linear dependence between tetragonality and the number of five-membered rings has been established. A natural bonding orbital analysis of the series of complexes is also presented.

Sonogashira cross-coupling and homocoupling on a silver surface:chlorobenzene and phenylacetylene on Ag(100)

Scanning tunneling microscopy, temperature-programmed reaction, near-edge X-ray absorption fine structure spectroscopy, and density functional theory calculations were used to study the adsorption and reactions of phenylacetylene and chlorobenzene on Ag(100). In the absence of solvent molecules and additives, these molecules underwent homocoupling and Sonogashira cross-coupling in an unambiguously heterogeneous mode. Of particular interest is the use of silver, previously unexplored, and chlorobenzene—normally regarded as relatively inert in such reactions. Both molecules adopt an essentially flat-lying conformation for which the observed and calculated adsorption energies are in reasonable agreement. Their magnitudes indicate that in both cases adsorption is predominantly due to dispersion forces for which interaction nevertheless leads to chemical activation and reaction. Both adsorbates exhibited pronounced island formation, thought to limit chemical activity under the conditions used and posited to occur at island boundaries, as was indeed observed in the case of phenylacetylene. The implications of these findings for the development of practical catalytic systems are considered.

A first principles analysis of the effect of hydrogen concentration in hydrogenated amorphous silicon on the formation of strained Si-Si bonds and the optical and mobility gaps

In this paper, we use a model of hydrogenated amorphous silicon generated from molecular dynamics with density functional theory calculations to examine how the atomic geometry and the optical and mobility gaps are influenced by mild hydrogen oversaturation. The optical and mobility gaps show a volcano curve as the hydrogen content varies from undersaturation to mild oversaturation, with largest gaps obtained at the saturation hydrogen concentration. At the same time, mid-gap states associated with dangling bonds and strained Si-Si bonds disappear at saturation but reappear at mild oversaturation, which is consistent with the evolution of optical gap. The distribution of Si-Si bond distances provides the key to the change in electronic properties. In the undersaturation regime, the new electronic states in the gap arise from the presence of dangling bonds and strained Si-Si bonds, which are longer than the equilibrium Si-Si distance. Increasing hydrogen concentration up to saturation reduces the strained bonds and removes dangling bonds. In the case of mild oversaturation, the mid-gap states arise exclusively from an increase in the density of strained Si-Si bonds. Analysis of our structure shows that the extra hydrogen atoms form a bridge between neighbouring silicon atoms, thus increasing the Si-Si distance and increasing disorder in the sample.

Characterization of Copper Covetic Bulk and Films: Copper with High Carbon Content

Incorporation of carbon nanostructures in metals is desirable to combine the strongly bonded electrons in the metal and the free electrons in carbon nanostructures that give rise to high ampacity and high conductivity, respectively. Carbon in copper has the potential to impact industries such as: building construction, power generation and transmission, and microelectronics. This thesis focuses on the structure and properties of bulk and thin films of a new material, Cu covetic, that contains carbon in concentrations up to 16 at.%. X-ray photoelectron spectroscopy (XPS) shows C 1s peak with both sp2 and sp3 bonded C measuring up to 3.5 wt.% (16 at.%). High resolution transmission electron microscopy and electron diffraction of bulk covetic samples show a modulated structure of ≈ 1.6 nm along several crystallographic directions in regions that have high C content suggesting that the carbon incorporates into the copper lattice forming a network. Electron energy loss spectra (EELS) from covetics reveal that the level of graphitization from the source material, activated carbon, is maintained in the covetic structure. Bulk Cu covetics have a slight increase in the lattice constant, as well as <111> texturing, or possibly a different structure, compared to pure Cu. Density functional theory calculations predict bonding between C and Cu at the edges and defects of graphene sheets. The electrical resistivity of bulk covetics first increases and then decreases with increasing C content. Cu covetic films were deposited using e-beam and pulsed laser deposition (PLD) at different temperatures. No copper oxide or any allotropes of carbon are present in the films. The e-beam films show enhanced electrical and optical properties when compared to pure Cu films of the same thickness even though no carbon was detected by XPS or EELS. They also have slightly higher ampacity than Cu metal films. EELS analysis of the C-K-edge in the PLD films indicate that graphitic carbon is transferred from the bulk into the films with uniform carbon distribution. PLD films exhibit flatter and higher transmittance curves and sheet resistance two orders of magnitude lower than e-beam films leading to a high figure of merit as transparent conductors.

Modeling and analysis of thermoelectric energy conversion efficiency in nanostructures.

116 p.

Enhanced oxidation activity from modified ceria: MnOx-ceria, CrOx-ceria and Mg doped VOx-ceria

Ceria is an important component of catalysts for oxidation reactions that proceed through the Mars-van Krevelen mechanism, promoting activity. A paradigm example of this is the VOx–CeO2 system for oxidative dehydrogenation reactions, where vanadium oxide species are supported on ceria and a special synergy between them is behind the enhanced activity: reduction of the catalyst is promoted by ceria undergoing reduction. This leads to favourable oxygen vacancy formation and hydrogen adsorption energies—useful descriptors for the oxidation activity of VOx–CeO2 catalysts. In this paper, we examine if this promoting effect on ceria-based catalysts holds for other metal oxide modifiers and we investigate MnOn– and CrOn–CeO2(111) (n = 0 − 4) as examples. We show, combining density functional theory calculations and statistical thermodynamics that similarly to the vanadia modifier, the stable species in each case is MnO2– and CrO2–CeO2. Both show favourable energetics for oxygen vacancy formation and hydrogen adsorption, indicating that VO2–CeO2 is not the only system of this type that can have an enhanced activity for oxidation reactions. However, the mechanism involved in each case is different: CrO2–CeO2 shows similar properties to VO2–CeO2 with ceria reduction upon oxygen removal stabilising the 5+ oxidation state of Cr. In contrast, with MnO2–CeO2, Mn is preferentially reduced. Finally, a model system of VO2–Mg:CeO2 is explored that shows a synergy between VO2 modification and Mg doping. These results shed light on the factors involved in active oxidation catalysts based on supported metal oxides on ceria that should be taken into consideration in a rational design of such catalysts.

Bulk structures of PtO and PtO(2) from density functional calculations

Platinum plays an important role in catalysis and electrochemistry, and it is known that the direct interaction of oxygen with Pt surfaces can lead to the formation of platinum oxides (PtO(x)), which can affect the reactivity. To contribute to the atomistic understanding of the atomic structure of PtO(x), we report a density functional theory study of the atomic structure of bulk PtO(x) (1 <= x <= 2). From our calculations, we identified a lowest-energy structure (GeS type, space group Pnma) for PtO, which is 0.181 eV lower in energy than the structure suggested by W. J. Moore and L. Pauling [J. Am. Chem. Soc. 63, 1392 (1941)] (PtS type). Furthermore, two atomic structures were identified for PtO(2), which are almost degenerate in energy with the lowest-energy structure reported so far for PtO(2) (CaCl(2) type). Based on our results and analysis, we suggest that Pt and O atoms tend to form octahedron motifs in PtO(x) even at lower O composition by the formation of Pt-Pt bonds.

Density-functional calculations of magnetoplasmons in quantum rings

We have studied the structure and dipole charge-density response of nanorings as a function of the magnetic field using local-spin-density-functional theory. Two small rings consisting of 12 and 22 electrons confined by a positively charged background are used to represent the cases of narrow and wide rings. The results are qualitatively compared with experimental data existing on microrings and on antidots. A smaller ring containing five electrons is also analyzed to allow for a closer comparison with a recent experiment on a two-electron quantum ring.