Riadh Sahnoun

Metal nanoparticles as models of single crystal surfaces and supported catalysts: Density functional study of size effects for CO/Pd(111)

Large octahedral and cuboctahedral palladium clusters, ranging from Pd55 to Pd146, have been investigated by means of all-electron relativistic density functional calculations. Adsorption of CO molecules on the (111) facets of these clusters was also studied. In particular, we focused on the interaction of CO (a single molecule per facet) with threefold hollow sites to inspect the variation of the calculated adsorption parameters with cluster size. We considered how observables calculated for that adsorption position on cluster facets relate to adsorption properties of the corresponding site at the single crystal surface Pd(111). We demonstrated for the first time that, with three-dimensional cluster models proposed here, one can reach cluster size convergence even for such a sensitive observable as the adsorption energy on a metal surface. We also addressed size effects on interatomic distances and the cohesive energy of bare Pd nanoclusters whose structure was fully optimized under the imposed Oh symmet...

Applying ultra-accelerated quantum chemical molecular dynamics technique for the evaluation of ligand protein interactions

Ligand–protein interactions have been studied using several chemical information techniques including quantum chemical methods that are applied to truncated systems composed of the ligand molecule and the surrounding amino acids of the receptor. Fragmented quantum molecular chemical studies are also a choice to study the enzyme–ligand system holistically, however there are still restrictions on the number of water molecules that can be included in a study of this nature. In this work we adopt a completely different approach to study ligand–protein interactions accounting explicitly for as many solvent molecules as possible and without the need for a fragmented calculation. Furthermore, we embed our quantum chemical calculations within a molecular dynamics framework that enables a fundamentally fast system for quantum chemical molecular dynamic simulations (QCMD). Central to this new system for QCMD is the tight binding QC system, newly developed in our laboratories, which combined with the MD paradigm results in an ultra-accelerated QCMD method for protein–ligand interaction evaluations. We have applied our newly developed system to the dihydrofolate reductase (DHFR)–methotrexate (MTX) system. We show how the proposed method leads us to new insights into the main interactions that bind MTX to the enzyme, mainly the interaction between the amino group of MTX and Asp27 of DHFR, as well as MTX amino group with Thr113 of DHFR, which have been only elucidated experimentally to date.

Effect of Surface Termination on Superlow Friction of Diamond Film: A Theoretical Study

We have applied molecular dynamics simulation and density functional theory calculations to analyze the effects of H and OH terminations on the frictional properties of diamond films at the atomistic and electronic levels. Molecular dynamics simulations were carried out for H-, OH-, and non-terminated diamond surfaces against an iron surface. Results of molecular dynamics simulations show that the frictional force is clearly decreased by the H or OH termination on the diamond surfaces. Moreover, results of density functional calculations show that a covalent bond is formed between Fe and C, while H- or OH-terminated diamond surfaces interact repulsively with an iron surface owing to antibonding interactions. We concluded that this interaction change between iron and diamond surfaces is the major contributing factor for achieving a low friction in H- or OH-terminated diamond.

Theoretical Study on Electronic and Electrical Properties of Nanostructural ZnO

The electronic and electrical properties of ZnO semiconductor single wall nanotube were investigated using periodic supercell approach within density functional theory combined with tight-binding quantum chemistry method. Armchair (10,10) and zigzag (10,0) nanotubes were considered. The lower strain energies required to roll up a ZnO graphitic sheet into a tube and the negative cohesive energies implied the possibility for the formation of ZnO single wall nanotubes. It was shown that the band gaps between the valence band maximum (VBM) and conduction band minimum (CBM) of nanotubes calculated by means of the two methods are similar and are larger than that of the bulk ZnO. It was found that the band gaps of ZnO nanotube are relatively insensitive to the chirality and diameter. According to the estimated electrical conductivities, the non-defect bulk and nanotube ZnO exhibited insulator properties, while they exhibited semiconductor properties when oxygen vacancies are introduced in the structures. The relative stability and band gap of fullerene-like ZnO clusters were also analyzed.

Theoretical investigation of the stability of highly charged C60 molecules produced with intense near-infrared laser pulses

We theoretically investigated the stability of highly charged C(60) (z+) cations produced from C(60) with an ultrashort intense laser pulse of lambda approximately 1800 nm. We first calculated the equilibrium structures and vibrational frequencies of C(60) (z+) as well as C(60). We then calculated key energies relevant to dissociation of C(60) (z+), such as the excess vibrational energy acquired upon sudden tunnel ionization from C(60). By comparing the magnitudes of the calculated energies, we found that C(60) (z+) cations up to z approximately 12 can be produced as a stable or quasistable (microsecond-order lifetime) intact parent cation, in agreement with the recent experimental report by V. R. Bhardwaj et al. [Phys. Rev. Lett. 93, 043001 (2004)] that almost only intact parent C(60) (z+) cations up to z=12 are detected by a mass spectrometer. The results of Rice-Ramsperger-Kassel-Marcus calculation suggest that the lifetime of C(60) (z+) drastically decreases by ten orders of magnitude as z increases from z=11 to z=13. Using the time-dependent adiabatic state approach, we also investigated the vibrational excitation of C(60) and C(60) (z+) by an intense near-infrared pulse. The results indicate that large-amplitude vibration with energy of >10 eV is induced in the delocalized h(g)(1)-like mode of C(60) (z+).

Hardware implementation of evolvable block-based neural networks utilizing a cost efficient sigmoid-like activation function

This paper presents the hardware implementation of an evolvable block-based neural network that utilizes a novel and cost efficient sigmoid-like activation function. Evolvable block-based neural networks (BbNNs) feature simultaneous optimization of structure, and viable implementation in reconfigurable digital hardware such as field programmable gate arrays (FPGAs). Efficient hardware implementation of BbNN structures is the primary goal of this paper. Various aspects of BbNN modeling and design considerations are presented. The neuron blocks are designed with properly described methodology, using only a single multiplier each, and implement a cost efficient sigmoid-like activation function. A novel method of reusing the multiplier to smoothly approximate a hyperbolic tangent (tanh) function to be used as the activation function for the neuron blocks is also presented. This is an important contribution, because a sigmoid-like activation function is provided at almost no additional cost. The neuron blocks are very cost efficient in terms of logic utilization when compared to the previous work. The BbNN is designed as an system-on-chip (SoC), and is functionally verified and tested on several case studies. The system performance allows real-time classification, and executes up to 410×faster than embedded software.

Quantum chemical studies for oxidation of morpholine by Cytochrome P450

Since morpholine oxidation has recently been shown to involve Cytochrome P450, the study on its mechanism at molecular level using quantum chemical calculations for the model of cytochrome active site is reported here. The reaction pathway is investigated for two electronic states, the doublet and the quartet, by means of density functional theory. The results show that morpholine hydroxylation occurs through hydrogen atom abstraction and rebound mechanism. However, in the low spin state, the reaction is concerted and hydrogen atom abstraction yields directly ferric-hydroxy morpholine complex without a distinct rebound step while in quartet state the reaction is stepwise. The presence of nitrogen in a morpholine heterocycle is postulated to greatly facilitate hydrogen abstraction. The hydroxylated product undergoes intramolecular hydrogen atom transfer from hydroxy group to nitrogen, leading to the cleavage of the C-N bond and the formation of 2-(2-aminoethoxy) acetaldehyde. The cleavage of the C-N bond is indicated as the rate-determining step for the studied reaction. The assistance of explicit water molecule is shown to lower the energy barrier for the C-N bond cleavage in enzymatic environment whereas solvent effects mimicked by COSMO solvent model have minor influence on relative energies along the pathway.

Development of Multiscale Simulator for Dye-Sensitized TiO2 Nanoporous Electrode Based on Quantum Chemical Calculation

In this study, we have developed a novel multiscale simulator for a dye-sensitized TiO2 porous electrode. In the simulator, we can estimate the properties of the dye-sensitized TiO2 porous electrode using the three-dimensional mesoscopic structure model constructed on the basis of our original porous structure simulator. The microscopic physical properties of the materials were estimated by quantum chemistry calculation using a tight-binding quantum chemical molecular dynamics program. From the calculation results, we determined the absorption coefficient and the diffusion coefficient of excited carriers used in the macroscopic simulation for photoelectrode characteristics. By using this multiscale simulator, we will be able to determine the best electrode system efficiently.

Host emission from BaMgAl10O17 and SrMgAl10O17 phosphor: Effects of temperature and defect level

— Understanding the mechanism of blue-light emission in Eu-doped BAM phosphor as well as its sensitive degradation is required because this is a very important material in fluorescent lamps and plasma-display panels. In this study, both theoretical and experimental investigations on the host emissions in BaMgAl10O17 and SrMgAl10O17 were performed. Host emissions from BaMgAl10O17 and SrMgAl10O17 by photoluminescence and thermoluminescence spectra were observed. Photoluminescence spectra suggested that the host emission from SrMgAl10O17 was easily quenched by thermal vibrations. The thermoluminescence spectra showed the existence of shallow and deep defect levels in BaMgAl10O17 and SrMgAl10O17 phosphors. It was shown that SrMgAl10O17 and its conduction plane could undergo degradation during irradiation of vacuum-ultra-violet (VUV) lights based on the calculated energy of formation of an oxygen vacancy. Moreover, the structural defects, such as oxygen vacancies, would cause localizing levels in the upper level in the valence band and in theconduction band. The results suggest the contribution of the host emission to the energy transfer to the Eu atoms would not be significant and the oxygen vacancies would act as the traps for excited carriers.

Simulation of electron diffusion in TiO2 porous structures in dye-sensitized solar cells

In order to understand the behavior of electrons in complex porous structures, we have simulated electron diffusion processes in complex porous structures that have been fabricated using a system for a three-dimensional porous structure simulator, POCO2. For a given porosity, as the overlap ratio representing a necked porous TiO2 structure increased, the coordination number of TiO2 particles increased, resulting in an increase in electron flux and a decrease in trapping time. To gain better insights, we simulated the diffusion of electrons using models with different particle size distributions. This study shows that for a narrower size distribution of TiO2 particles, a better electron diffusion process is realized. This result can be ascribed to the formation of a better TiO2 coordination network. Consequently, through this study, we have shown that a well-formed neck between TiO2 particles improves the electron diffusion properties of a complex porous material.