Density Functional Theory (DFT) with B3LYP/6-311++g** level has been performed to investigate the electronic structures of cage B12Hn for up to n <= 12 and AlB12Hn for up to n <= 13. Moreover, the computations has been extended to the charged clusters of [B12H12](q), [AlB12H12](q) and [AlB12H13](q) where (q = +/- 1 and +/- 2). Their energetics are calculated and structural analysis have been carried out. Cage form of the B-12 remains stable against to hydrogen adsorptions. Copyright (C) 2011, Hydrogen Energy Publications, LLC. Published by Elsevier Ltd. All rights reserved.

All the channels of the reaction dynamics of gas-phase H (or D) atoms with D (or H) atoms adsorbed onto a Cu(111) surface have been studied by quasiclassical constant energy molecular dynamics simulations. The surface is flexible and is prepared at different temperature values, such as 30 K, 94 K, and 160 K. The adsorbates were distributed randomly on the surface to create 0.18 ML, 0.28 ML, and 0.50 ML of coverages. The multi-layer slab is mimicked by a many-body embedded-atom potential energy function. The slab atoms can move according to the exerted external forces. Treating the slab atoms non-rigid has an important effect on the dynamics of the projectile atom and adsorbates. Significant energy transfer from the projectile atom to the surface lattice atoms takes place especially during the first impact that modifies significantly the details of the dynamics of the collisions. Effects of the different temperatures of the slab are investigated in this study. Interaction between the surface atoms and the adsorbates is modeled by a modified London-Eyring-Polanyi-Sato (LEPS) function. The LEPS parameters are determined by using the total energy values which were calculated by a density functional theory and a generalized gradient approximation for an exchange-correlation energy for many different orientations, and locations of one- and two-hydrogen atoms on the Cu(111) surface. The rms value of the fitting procedure is about 0.16 eV. Many different channels of the processes on the surface have been examined, such as inelastic reflection of the incident hydrogen, subsurface penetration of the incident projectile and adsorbates, sticking of the incident atom on the surface. In addition, hot-atom and Eley-Rideal direct processes are investigated. The hot-atom process is found to be more significant than the Eley-Rideal process. Furthermore, the rate of subsurface penetration is larger than the sticking rate on the surface. In addition, these results are compared and analyzed as a function of the surface temperatures.

Density functional theory (DFT) B3LYP at 6-311++G(d,p) level is employed to optimize the structures of AlBn (n = 1-14) microclusters. Analysis of the energetic and structural stability of these clusters and their various isomers are presented. Total and binding energies of the clusters have been calculated. Their harmonic frequencies, point symmetries, and the highest occupied molecular orbital-lowest unoccupied molecular orbital (HOMO-LUMO) energy gaps have been determined. Results are evaluated by comparing to the previous similar works. (C) 2011 Elsevier B.V. All rights reserved.

The biologically important 2-amino-3-hydroxypyridine reacts with benzoyl chloride to give 2-(N-benzoylbenzamido)pyridine-3-yl benzoate. This synthesized compound has been studied by elemental analysis, X-ray crystallography and also theoretically by density functional theory (DFT) framework with B3LYP/6-311++G(d, p) level of theory. The molecules of this compound crystallize in the orthorhombic space group of P212121 and the crystal packing involves both hydrogen-bonding and C–H⋯π interaction. The vibrational normal modes of the molecular structure are investigated by ab initio method for both infrared intensities (IR) and for Raman activities. Furthermore, the corresponding assignments are discussed. Hydrogen and carbon atoms of the benzene rings are found to be highly active. Also, experimentally obtained IR spectrum is presented and compared with the available theoretical data. Experimentally and theoretically obtained IR spectrum are in good agreement.

A novel application for detecting specific biomolecules using SWNT-ssDNA nanohybrid is described. SWNT-ssDNA hybrid is formed by conjugating amino-ended single strand of DNA (ssDNA) with carboxylic group modified SWNTs through a straightforward EDC coupling reaction. ssDNA functionalized SWNT hybrids could be used as high fidelity sensors for biomolecules. The sensing capability is demonstrated by the change in the electronic properties of SWNT. Employing DNA functionalized SWNT FETs could lead to dramatically increased sensitivity in biochemical sensing and medical diagnostics applications.

In this work constant energy molecular dynamics simulations are achieved for investigating sputtering process of Ar + Ni(1 0 0) collision system. The Ni crystal is imitated by an embedded-atom potential, whereas the interaction between the projectile and the surface is modeled by re-parameterized ZBL potential. Seven hundred eighty-four Ar atoms carrying 20–50 eV are sent towards a Ni(1 0 0) surface at normal incidence. Each projectile meets with different initial coordinates (phase) of the nickel atoms because of thermal vibrations in the slab. Effects of the different initial phases of the surface are compared with the available theoretical and experimental data.

An analytical embedded atom method which can treat bcc transition metal iron has been developed. In this model, a new potential was presented and a modified term has been introduced to fit the negative Cauchy pressure P-C = (C-12 - C-44)/2 for Fe element. The new model was applied to calculate thermodynamic properties of binary alloys of the bcc transition metals: Fe, V and Cr. The calculated dilute-solution enthalpies and formation enthalpies of random alloys are in good agreement with the results of first principles calculations and that of the thermodynamic calculations. (C) 2009 Elsevier B.V. All rights reserved.

This article has been retracted: please see Elsevier Policy on Article Withdrawal (http://www.elsevier.com/locate/withdrawalpolicy). This article has been retracted at the request of the editor. The authors have plagiarized part of a paper that had already appeared in Z. Phys. B., 101 (1996) 161–168. One of the conditions of submission of a paper for publication is that authors declare explicitly that their work is original and has not appeared in a publication elsewhere. Re-use of any data should be appropriately cited. As such this article represents a severe abuse of the scientific publishing system. The scientific community takes a very strong view on this matter and apologies are offered to readers of the journal that this was not detected during the submission process.

An analytical embedded atom method which can treat bcc transition metal iron has been developed. In this model, a new potential was presented and a modified term has been introduced to fit the negative Cauchy pressure P-C = (C-12 - C-44)/2 for Fe element. The new model was applied to calculate thermodynamic properties of binary alloys of the bcc transition metals: Fe, V and Cr. The calculated dilute-solution enthalpies and formation enthalpies of random alloys are in good agreement with the results of first principles calculations and that of the thermodynamic calculations. (C) 2009 Elsevier B.V. All rights reserved.

In recent years fractional calculus has played an important role in various fields such as mechanics, electricity, chemistry, biology, economics, modeling, identification, control theory and signal processing. The scope of this book is to present the state of the art in the study of fractional systems and the application of fractional differentiation. Furthermore, the manufacture of nanowires is important for the design of nanosensors and the development of high-yield thin films is vital in procuring clean solar energy. This wide range of applications is of interest to engineers, physicists and mathematicians.

Boron is an element that has ability to build strong and highly directional bonds with boron itself. As a result, boron atoms form diverse structural motifs, ultimately can yield distinct nano structures, such as planar, quasi-planar, convex, cage, open-cage, tubular, spherical., ring, dome-like, shell, capsule, and so on, i.e., it can take almost any shape. Therefore, a deep understanding of the physical and chemical properties becomes important in boron cluster chemistry. Electronic and geometric structures, total and binding energies, harmonic frequencies, point symmetries, charge distributions, dipole moments, chemical bondings and the highest occupied molecular orbital-lowest unoccupied molecular orbital energy gaps of neutral B-n (n=13-20) clusters have been investigated by, density functional theory (DFT), B3LYP with 6-311++G(d,p) basis set. Furthermore, the first and the second energy differences are used to obtain the most stable sizes. We have observed that almost all physical properties are size dependent, and double-ring tubular form of B-20 has the highest binding energy per atom. The icosahedral structure with an inside atom is found as impossible as a stable structure for the size thirteen. This structure transforms to an open-cage form. The structural transition from two-dimensional to three-dimensional is found at the size of 20 and consistent with the literature. The calculated charges by the Mulliken analysis show that there is a symmetry pattern with respect to the x-z and y-z planes for the charge distributions. The unusual planar stability of the boron clusters may be explained by the delocalized pi and sigma bonding characteristic together with the existence of the multicentered bonding. The results have been compared to available studies in the literature.

Boron is an element that has ability to build strong and highly directional bonds with boron itself. As a result, boron atoms form diverse structural motifs, ultimately can yield distinct nano structures, such as planar, quasi-planar, convex, cage, open-cage, tubular, spherical, ring, dome-like, shell, capsule, and so on, i.e., it can take almost any shape. Therefore, a deep understanding of the physical and chemical properties becomes important in boron cluster chemistry. Electronic and geometric structures, total and binding energies, harmonic frequencies, point symmetries, charge distributions, dipole moments, chemical bondings and the highest occupied molecular orbitallowest unoccupied molecular orbital energy gaps of neutral Bn (n = 1320) clusters have been investigated by density functional theory (DFT), B3LYP with 6311+ + G(d,p) basis set. Furthermore, the first and the second energy differences are used to obtain the most stable sizes. We have observed that almost all physical properties are size dependent, and double-ring tubular form of B20 has the highest binding energy per atom. The icosahedral structure with an inside atom is found as impossible as a stable structure for the size thirteen. This structure transforms to an open-cage form. The structural transition from two-dimensional to three-dimensional is found at the size of 20 and consistent with the literature. The calculated charges by the Mulliken analysis show that there is a symmetry pattern with respect to the x-z and y-z planes for the charge distributions. The unusual planar stability of the boron clusters may be explained by the delocalized and bonding characteristic together with the existence of the multicentered bonding. The results have been compared to available studies in the literature.

The geometries, stabilities, and energetics of aluminum doped boron clusters, up to 13-atom, and their various hydrogenated complexes have been investigated via the density functional theory (DFT). The geometry optimizations have been carried out by using B3LYP functional and 6-311++G11 basis set. Up to 5-atom clusters arrangements of the atoms, in the most stable structures, have two-dimensional forms. From 6- to 13-atom clusters three-dimensional forms are favored by the lowest energy structures. Hydrogen hosting effects the structures of AlBn clusters. Adding an Al atom to the cage B12 leads structural changes but hydrogenated boron, B12H12 can resist to Al effect.

Using Molecular Dynamics and thermal quenching simulations the stable geometrical structures and energies of Cun (n=21-71) clusters are identified. The interaction between the cluster atoms is modeled by an EmbeddedAtom Potential Surface, Voter and Chen's version. The stable geometrical structures and energies are obtained from 500 phase space coordinates generated along high-energy trajectories. The internal energy (about T=2500 K) is above the melting temperature of the Cun clusters. The thermal quenching technique is employed to remove slowly the internal kinetic energy of the clusters. Because of this slow minimization process the locally stable isomers are separated from those meta-stable ones.

In this study, we have used London–Eyring–Polanyi–Sato (LEPS) functional form as an interaction potential energy function to simulate H (2H)→Cu(111) interaction system. The parameters of the LEPS function are determined in order to analyze reaction dynamics via molecular dynamics computer simulations of the Cu(111) surface and H/(2H) system. Nonlinear least-squares method is used to find the LEPS parameters. For this purpose, we use the energy points which were calculated by a density-functional theory method with the generalized gradient approximation including exchange-correlation energy for various configurations of one and two hydrogen atoms on the Cu(111) surface. After the fitting procedures, two different parameters sets are obtained that the calculated root-mean-square values are close to each other. Using these sets, contour plots of the potential energy surfaces are analyzed for H→Cu(111) and 2H→Cu(111) interactions systems. In addition, sticking, penetration, and scattering sites on the surface are analyzed by using these sets.

The sputtering process of Ar+Ni(100) collision systems is investigated by means of constant energy molecular dynamics simulations. The Ni(100) slab is mimicked by an embedded-atom potential, and the interaction between the projectile and the surface is modelled by using the reparametrized ZBL potential. Ni atom emission from the lattice is analysed over the range of 20–50 eV collision energy. Sputtering yield, angular and energy distributions of the scattered Ar and of the sputtered Ni atoms are calculated, and compared to the available theoretical and experimental data.

Dissociative chemisorption probabilities for H 2 (v, j) + Ni(100) collision systems have been estimated by using Artificial Neural Network (ANN). For training, previously determined probability values via molecular dynamics simulations have been used. Performance of the ANN, for predicting any quantities in the molecule-surface interaction, has been investigated. Effects of the surface sites and the rovibrational states of the molecule on the process are analyzed. The results are in good agreement with the related previous studies.

An Ar+-Ni(1 0 0) collision system at 1 keV impact energy was investigated by using realistic isoenergetic molecular dynamics (MD) simulations. The sputtering process upon Ar+ ion impact and damage to the Ni(1 0 0) surface are examined in detail. Studying of high bombarding energy regions leads to the necessity of larger and thick enough slabs, otherwise incoming ions can easily pass through the slab; as a result, investigated physical properties may not be revealed. In addition the simulation time should be long enough to observe and to calculate a reliable macroscopic property such as sputtering yield that is addressed in this study. In order to preserve the total energy in the simulation at this collision energy a small time-step (0.1 fs) is used. We have made use of our developed linear scaling parallel MD program to overcome these demands. The Ni(1 0 0) slab is formed by 63700 atoms (122 angstrom x 122 angstrom x 44 angstrom) and the total observation time for each collision event is about 2.25 ps. Several properties such as penetration depths, angular and energy distributions of the reflected Ar and sputtered Ni atoms as well as dissociation time, embedded, scattering, sputtering patterns and geometries of the sputtered clusters are also reported, and the calculated sputtering yield is found to be in good agreement with the available experimental results.