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

Electronic structure of copper nitrides as a function of nitrogen content

he nitrogen content dependence of the electronic properties for copper nitride thin films with an atomic percentage of nitrogen ranging from 26 ± 2 to 33 ± 2 have been studied by means of optical (spectroscopic ellipsometry), thermoelectric (Seebeck), and electrical resistivity measurements. The optical spectra are consistent with direct optical transitions corresponding to the stoichiometric semiconductor Cu3N plus a free-carrier contribution, essentially independent of temperature, which can be tuned in accordance with the N-excess. Deviation of the N content from stoichiometry drives to significant decreases from − 5 to − 50 μV/K in the Seebeck coefficient and to large enhancements, from 10− 3 up to 10 Ω cm, in the electrical resistivity. Band structure and density of states calculations have been carried out on the basis of the density functional theory to account for the experimental results.

Optical absorption analysis of quaternary molybdate- and tungstate-ordered double perovskites

Quaternary-ordered double perovskite A2MM’O6 (M=Mo,W) semiconductors are a group of materials with a variety of photocatalytic and optoelectronic applications. An analysis focused on the optoelectronic properties is carried out using first-principles density-functional theory with several U orbital-dependent one-electron potentials applied to different orbital subspaces. The structural non-equivalence of the atoms resulting from the symmetry has been taken in account. In order to analyze optical absorption in these materials deeply, the absorption coefficients have been split into inter- and intra-non-equivalent species contributions. The results indicate that the effect of the A and M’ atoms on the optical properties are minimal whereas the largest contribution comes from the non-equivalent O atoms to M transitions.

Self-consistent relativistic band structure of the CH3NH3PbI3 perovskite

The electronic structure and properties of the orthorhombic phase of the CH 3 NH 3 PbI 3 perovskite are computed with density functional theory. The structure, optimized using a van der Waals functional, reproduces closely the unit cell volume. The experimental band gap is reproduced accurately by combining spin-orbit effects and a hybrid functional in which the fraction of exact exchange is tuned self-consistently to the optical dielectric constant. Including spin-orbit coupling strongly reduces the anisotropy of the effective mass tensor, predicting a low electron effective mass in all crystal directions. The computed binding energy of the unrelaxed exciton agrees with experimental data, and the values found imply a fast exciton dissociation at ambient temperature. Also polaron masses for the separated carriers are estimated. The values of all these parameters agree with recent indications that fast dynamics and large carrier diffusion lengths are key in the high photovoltaic efficiencies shown by these materials.

Analysis of SnS2 hyperdoped with V proposed as efficient absorber material

Intermediate-band materials can improve the photovoltaic efficiency of solar cells through the absorption of two subband-gap photons that allow extra electron-hole pair formations. Previous theoretical and experimental findings support the proposal that the layered SnS2 compound, with a band-gap of around 2 eV, is a candidate for an intermediate-band material when it is doped with a specific transition-metal. In this work we characterize vanadium doped SnS2 using density functional theory at the dilution level experimentally found and including a dispersion correction combined with the site-occupancy-disorder method. In order to analyze the electronic characteristics that depend on geometry, two SnS2 polytypes partially substituted with vanadium in symmetry-adapted non-equivalent configurations were studied. In addition the magnetic configurations of vanadium in a SnS2 2H-polytype and its comparison with a 4H-polytype were also characterized. We demonstrate that a narrow intermediate-band is formed, when these dopant atoms are located in different layers. Our theoretical predictions confirm the recent experimental findings in which a paramagnetic intermediate-band material in a SnS2 2H-polytype with 10% vanadium concentration is obtained.

Femtosecond observation of benzyne intermediates in a molecular beam: Bergman rearrangement in the isolated molecule

In this communication, we report our femtosecond real-time observation of the dynamics for the three didehydrobenzene molecules (p-, m-, and o-benzyne) generated from 1,4-, 1,3-, and 1,2-dibromobenzene, respectively, in a molecular beam, by using femtosecond time-resolved mass spectrometry. The time required for the first and the second C-Br bond breakage is less than 100 fs; the benzyne molecules are produced within 100 fs and then decay with a lifetime of 400 ps or more. Density functional theory and high-level ab initio calculations are also reported herein to elucidate the energetics along the reaction path. We discuss the dynamics and possible reaction mechanisms for the disappearance of benzyne intermediates. Our effort focuses on the isolated molecule dynamics of the three isomers on the femtosecond time scale.

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.

The hard-soft acid-base principle in enzymatic catalysis: dual reactivity of phosphoenolpyruvate.

In this paper, the chemical reactivity of C3 of phosphoenolpyruvate (PEP) has been analyzed in terms of density functional theory quantified through quantum chemistry calculations. PEP is involved in a number of important enzymatic reactions, in which its C3 atom behaves like a base. In three different enzymatic reactions analyzed here, C3 sometimes behaves like a soft base and sometimes behaves like a hard base in terms of the hard-soft acid-base principle. This dual nature of C3 of PEP was found to be related to the conformational change of the molecule. This leads to a testable hypothesis: that PEP adopts particular conformations in the enzyme-substrate complexes of different PEP-using enzymes, and that the enzymes control the reactivity through controlling the dihedral angle between the carboxylate and the C==C double bond of PEP.

Estudo da cristalinidade de filmes finos de nitreto de índio e simulado pelo pacote de programas Wien2k

Neste trabalho, foi utilizado o método de deposição assistida por feixe de íons (IBAD na sigla em inglês) para produção de filmes finos de nitreto de índio em substratos de silício (111) e Safira-C. Variando as condições de deposição e utlilizando a técnica de difração de raios-X, investigou-se com o intuito de obter os parâmetros que resultam em filmes finos com melhor grau de cristalinidade. Os filmes produzidos a 380C apresentaram alta cristalinidade, superior àqueles a 250C. Temperaturas muito superiores a 380C não ocasionam a formação de filme cristalino de InN, como foi observado ao utilizar a temperatura de 480C; o mesmo se observa ao utilizar temperatura ambiente. Na temperatura considerada adequada ,de 380C, obteve-se que a utilização de Ra, ou seja, a razão de fluxo de partículas entre o nitrogênio e índio, em torno de 2,3 permite obter um melhor grau de cristalinização, o qual decresce conforme se diverge desse valor. A comparação entre difratogramas de amostras produzidas com e sem a evaporação prévia de titânio, o qual é possível observar um deslocamento dos picos do InN, indicam que o efeito Gettering permite a redução de impurezas no filme, principalmente de oxigênio. Utilizou-se a técnica de Retroespalhamento de Rutherford para obtenção da composição dos elementos e o perfil de profundidade. Notou-se uma forte mistura dos elementos do substrato de silício e safira com o nitreto de índio mesmo próximos a superfície. A presença indesejável de impurezas, principalmente o oxigênio, durante a deposição de filmes finos é praticamente inevitável. Desta forma, cálculos ab initio baseados na Teoria do Funcional da Densidade (DFT) foram realizados para investigar defeitos isolados e complexos de oxigênio no nitreto de índio e a sua influência nas propriedades óticas. Considerou-se diferentes concentrações de oxigênio (x=2,76, 8,32, 11,11 e 22,22%) aplicando-se o método PBEsolGGA e TB-mBJ para o tratamento da energia e potencial de troca e correlação. Obteve-se que é energeticamente favorável o oxigênio existir principalmente como defeito carregado e isolado. Os resultados utilizando a aproximação de TB-mBJ indicam um estreitamento do bandgap conforme a concentração de oxigênio aumenta. Entretanto, a alta contribuição do efeito de Moss-Burstein resulta num efetivo alargamento do band gap, gerando valores de band gap ótico maiores que no do bulk de nitreto de índio.

Propriedades magnéticas de trímeros de FexCo1-x depositados em Pt(111)

Quais propriedades magnéticas são modificadas quando se agrupam átomos de Fe/Co para formar estruturas quasi-2D, se comparadas aos nanofios (quasi-1D) de FexCo1-x? E como estas propriedades reagem com a variação da proporção de Fe/Co nos aglomerados? A fim de responder a estas questões, trímeros de FexCo1-x depositados em Pt(111) são investigados utilizando o método de primeiros princípios Real Space-Linear Muffin-Tin Orbital-Atomic Sphere Approximation (RS-LMTO-ASA) no âmbito da Teoria do Funcional da Densidade (DFT). Diferentes configurações de trímeros triangulares são consideradas, variando-se as posições e a concentração dos átomos de Fe/Co. Neste trabalho, demonstra-se a ocorrência de uma tendência não-linear estritamente decrescente dos momentos orbitais médios como função da concentração de Fe, distinta do encontrado tanto para os nanofios de FexCo1-x (dependência linear) quanto para a monocamada correspondente (dependência não-linear). Os resultados obtidos mostram ainda que os momentos orbitais variam com o ambiente local e com a direção de magnetização, especialmente quando associados aos átomos de Co, em concordância com publicações anteriores. A mudança de dimensionalidade quasi-1D (nanofios) para quasi-2D (trímeros compactos) não afeta o comportamento dos momentos de spin, que permanecem descritos por uma função linear com respeito à proporção de Fe/Co. Ambos o formato e a concentração de Fe nos sistemas apresentam um papel importante nos valores de energia de anisotropia magnética. Em adição, observou-se que o subtrato de Pt opera ativamente na definição das propriedades magnéticas dos aglomerados. Embora todas as configurações lineares e compactas dos aglomerados de FexCo1-x sejam estáveis e exibam interações fortemente ferromagnéticas entre os primeiros vizinhos, nem todas revelaram o ordenamento colinear como estado fundamental, apresentando uma interação de Dzyaloshinskii-Moriya não-desprezível induzida pelo acoplamento spin-órbita. Estes casos específicos são: o trímero triangular de Co puro e o trímero linear (nanofio) de Fe puro, para o qual foi verificado o acoplamento do tipo Ruderman-Kittel-Kasuya-Yosida entre os átomos de Fe constituintes. Os resultados obtidos contribuem para o entendimento de quais mecanismos definem o magnetismo nos trímeros de FexCo1-x/Pt(111), e discutem as questões presentes atualmente na literatura no contexto destes sistemas.

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.

Mechanical annealing of metallic electrodes at the atomic scale

The process of creating an atomically defined and robust metallic tip is described and quantified using measurements of contact conductance between gold electrodes and numerical simulations. Our experiments show how the same conductance behavior can be obtained for hundreds of cycles of formation and rupture of the nanocontact by limiting the indentation depth between the two electrodes up to a conductance value of approximately 5G0 in the case of gold. This phenomenon is rationalized using molecular dynamics simulations together with density functional theory transport calculations which show how, after repeated indentations (mechanical annealing), the two metallic electrodes are shaped into tips of reproducible structure. These results provide a crucial insight into fundamental aspects relevant to nanotribology or scanning probe microscopies.

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.

Theoretical insights on electron donor-acceptor interactions involving carbon dioxide

Electron donor-acceptor (EDA) interactions are widely involved in chemistry and their understanding is essential to design new technological applications in a variety of fields ranging from material sciences and chemical engineering to medicine. In this work, we study EDA complexes of carbon dioxide with ketones using several ab initio and Density Functional Theory methods. Energy contributions to the interaction energy have been analyzed in detail using both variational and perturbational treatments. Dispersion energy has been shown to play a key role in explaining the high stability of a non-conventional structure, which can roughly be described by a cooperative EDA interaction.