Development of the ReaxFF Reactive Force Field for Inherent Point Defects in the Si/Silica System.

We redeveloped the ReaxFF force field parameters for Si/O/H interactions that enable molecular dynamics (MD) simulations of Si/SiO2 interfaces and O diffusion in bulk Si at high temperatures, in particular with respect to point defect stability and migration. Our calculations show that the new force field framework (ReaxFFpresent), which was guided by the extensive quantum mechanical-based training set, describes correctly the underlying mechanism of the O-migration in Si network, namely, the diffusion of O in bulk Si occurs by jumping between the neighboring bond-centered sites along a path in the (110) plane, and during the jumping, O goes through the asymmetric transition state at a saddle point. Additionally, the ReaxFFpresent predicts the diffusion barrier of O-interstitial in the bulk Si of 64.8 kcal/mol, showing a good agreement with the experimental and density functional theory values in the literature. The new force field description was further applied to MD simulations addressing O diffusion in bulk Si at different target temperatures ranging between 800 and 2400 K. According to our results, O diffusion initiates at the temperatures over 1400 K, and the atom diffuses only between the bond-centered sites even at high temperatures. In addition, the diffusion coefficient of O in Si matrix as a function of temperature is in overall good agreement with experimental results. As a further step of the force field validation, we also prepared amorphous SiO2 (a-SiO2) with a mass density of 2.21 gr/cm3, which excellently agrees with the experimental value of 2.20 gr/cm3, to model a-SiO2/Si system. After annealing the a-SiO2/Si system at high temperatures until below the computed melting point of bulk Si, the results show that ReaxFFpresent successfully reproduces the experimentally and theoretically defined diffusion mechanism in the system and succeeded in overcoming the diffusion problem observed with ReaxFFSiOH(2010), which results in O diffusion in the Si substrate even at the low temperature such as 300 K.

Structural Properties of Pristine and Defected ZnO Nanosheets Under Biaxial Strain: Molecular Dynamics Simulations.

Structural properties of defected zinc oxide nanosheets have been investigated by performing classical molecular dynamics simulations. An atomistic potential energy function has been used to represent the interactions among the atoms. Different types of defects (vacancy, exchange, Stone-Wales like, line defect and ring-like) at the central region have been considered for the nanosheets. Strain has been applied to the generated ZnO nanostructures along both x- and y-axes, which has been realized at two different temperatures, 1 and 300 K. It has been found that ZnO nanosheets following strain application undergo a structural change depending on the temperature, type of the defect and the absence or presence of periodic boundaries. The rate of strain applied also plays an important role in the structural properties of the defected ZnO nanosheets.

Structural properties of ZnO nanotubes under uniaxial strain: molecular dynamics simulations.

Structural properties of zinc oxide nanotubes with zigzag, armchair and chiral geometries have been investigated by performing classical molecular dynamics simulations. An atomistic potential energy function has been used to represent the interactions among the atoms. Strain has been applied to the generated ZnO nanostructures along their length, which has been realized at two different temperatures, 1 K and 300 K. It has been found that ZnO nanostructures following strain application undergo a structural change depending on temperature, geometry and tube radius.

Quantum chemical treatment of beta-sitosterol molecule.

Beta-sitosterol is used as a dietary supplement for lowering plasma cholesterol, and has atherosclerosis preventive, anti-inflammatory, antimicrobial, antipyretic, induced apoptosis, and anticancer effects. In order to understand the effect of the molecule we have investigated the molecule theoretically. The structural, vibrational, and electronic properties of the beta-sitosterol molecule have been investigated theoretically by performing molecular mechanics (MM+ force field), semiempirical self-consistent-field molecular-orbital (PM3), and density functional theory (B3LYP) calculations. The geometry of the considered molecule has been optimized; the vibrational dynamics and the electronic properties have been calculated in its ground state in the gas phase. The optimized structure of the molecule is not planar, and its heat of formation is exothermic. The calculated infrared spectrum for beta-sitosterol agrees well qualitatively with the experimentally determined FTIR spectrum. The interfrontier molecular orbitals are localized mainly on the double C-C bond, and the energy difference of the corresponding orbitals is relatively small, which makes the molecule kinetically stable. According to the calculated dipole moment, beta-sitosterol is a polar molecule. The calculated results for the beta-sitosterol molecule in the present study will aid in elucidation of the mechanism of action and may further be used in lipid metabolism drug design studies.

On the SmCo dimer: a detailed density functional theory analysis.

Making use of 21 different exchange-correlation functionals, we performed density functional theory calculations, within the effective core potential level, to investigate some spectroscopic and electronic features of the SmCo dimer in its ground state. A particular emphasis was placed on the (spin) multiplicity of SmCo. Most of the functionals under discussion unanimously agreed that the multiplicity of SmCo should be 10. It was observed that the nature of interaction between Sm and Co atoms to form the SmCo dimer can be described, to a good approximation, by a Lennard-Jones curve. For the multiplicity value 10, the binding energy D(e) was seen to be in the range 1.08-1.77 eV, while the equilibrium separation distance and the fundamental frequency were found to be r(e) = 2.975 +/- 0.035 A and omega(e) = 120 +/- 10 cm(-1), respectively.

Quantum chemical investigation of nitrotyrosine (3-nitro-L-tyrosine) and 8-nitroguanine.

The structural, vibrational and electronic properties of nitrotyrosine and 8-nitroguanine have been investigated theoretically by performing the molecular mechanics (MM+ force field), the semi-empirical self-consistent-field molecular-orbital (PM3), and density functional theory calculations. The geometry of the nitrotyrosine and 8-nitroguanine molecules have been optimized, the vibrational dynamics and the electronic properties calculated in their ground states in the gas phase.

Functionality of C(4,4) carbon nanotube as molecular detector.

Alterations in the electronic transport properties of C(4,4) single walled carbon nanotube when an agent is introduced to the outer surface are investigated theoretically. Several chemical agents in this context are investigated. The calculations are performed in two steps: First an optimized geometry for the functionalized carbon nanotube is obtained using semi-empirical calculations at the PM3 level, and then the transport relations are obtained using non equilibrium green-function approach. Gaussian and Transiesta-C simulation packages are used in the calculations correspondingly. The "electrodes" are chosen to be ideal geometry of the particular carbon nanotube, eliminating current quantization effects due to contact region. By varying chemical potential in the electrode regions, an I-V curve is traced for each particular functionalisation. Conductance in carbon nanotubes show a strong dependence on the geometry and aromaticity, both are which altered when the suitable agent is introduced. This dependence results in rather dramatic response in the I-V trace, the current is reduced significantly, and quantization effects are observed, even for a single molecule. However due to chemically stable nature, not all agents form a chemical bond to the surface. Overall, the material is a promising candidate for detector equipment.

Li+ and Li interactions with carbon nanocage structures.

Molecular dynamics simulations have been carried out to explore the structural properties of Li and Li+ confined inside single-walled carbon nanotubes (SWCNTs) and fullerene molecules. C-Li, C-Li+, Li-Li and Li+-Li+ interactions have been represented by pair functions and parameterized for the corresponding interactions. C-C interactions have been modeled by Tersoff potential. Open-ended SWCNTs with various sizes and chirality, as well as fullerenes with various sizes have been considered in the simulations. C-Li interaction is stronger than that of C-Li+. Endohedral Li+ doping caused structural deformations in C60. It has been found that for both Li and Li+ cases endohedral doping is favorable with respect to exohedral doping. This result is valid for both fullerenes and nanotubes.

An algorithm for constructing various kinds of nanojunctions using zig-zag and armchair nanotubes.

A method for generating various forms of junctions involving armchair and zig-zag nanotubes, firstly introduced by Zsoldos et al., is developed to cover all types of armchair and zig-zag nanotubes in a systematical way. This method can also be used to produce nanogears and toothed canals. The method is explained and flowcharts are included to aid in programming into a code.

Density functional theory calculations for [C(2)H(4)N(2)O(6)]((n)) (n=0, +1, -1).

The structural and electronic properties of neutral and mono ionic structures of isolated ethylene glycol dinitrate (EGDN) [C(2)H(4)N(2)O(6)]((n)) (n=0, +1, -1) have been investigated by performing density functional theory calculations at B3LYP level. The optimum geometry, vibrational frequencies, electronic structure and some thermo dynamical values of the structures considered have been obtained in their ground states. The calculations reveal that as the charge develops the bond lengths and angles change. In the anionic case charge accumulation causes NO(2) elimination as a result of esteric O-N bond cleavage.

Thermal stability of benzorods: molecular-dynamics simulations.

Thermal stability of benzorods 2C6-20C6, which are obtained by stacking n (n=2-20) dehydrogenated benzene, have been investigated by molecular-dynamics simulations. It has been found that these structures assume a geometrical form depending on the number of dehydrogenated benzene layers, and they are stable under heat treatment up to elevated temperatures with a dependence on length.

Stability of C60 chains: molecular dynamics simulations.

A linearly aligned structure of three C60 fullerene, interconnected by two benzorods of same size, have been investigated under heat treatment. The overall structure resembles a section of a beaded string. Nine different lengths of benzorods have been considered, and the effect on the thermal stability have been investigated by means of molecular dynamics method. It has been found that the structure is thermally stable up to elevated temperatures, and the linear alignment of the structure is persistent, up to the temperature of decomposition.