Ab Initio Calculations of Structural Evolution and Conductance of Benzene-1,4-dithiol on Gold Leads

By performing at) initio density functional theory (DFT) calculations and electronic transport simulations based on the OFT nonequilibrium Green`s functions method we investigate how the conformational changes of a benzene-1,4-dithiol molecule bonded to gold affect the molecular transport as the electrodes are separated from each other. In particular we consider the full evolution of the stretching process until the Junction breaking point and compare results obtained with a standard semilocal exchange and correlation functional to those computed with a self-interaction corrected method. We conclude that the inclusion of self-interaction corrections is fundamental for describing both the molecule conductance and its stability against conformational fluctuations.

Tight-binding model for carbon nanotubes from ab initio calculations

Here we present a parametrized tight-binding (TB) model to calculate the band structure of single-wall carbon nanotubes (SWNTs). On the basis of ab initio calculations we fit the band structure of nanotubes of different radii with results obtained with an orthogonal TB model to third neighbors, which includes the effects of orbital hybridization by means of a reduced set of parameters. The functional form for the dependence of these parameters on the radius of the tubes can be used to interpolate appropriate TB parameters for different SWNTs and to study the effects of curvature on their electronic properties. Additionally, we have shown that the model gives an appropriate description of the optical spectra of SWNTs, which can be useful for a proper assignation of SWNTs` specific chirality from optical absorption experiments.

Electric field gradients in (111)In-doped (Hf/Zr)(3)Al(2) and (Hf/Zr)(4)Al(3) mixed compounds: ab initio calculations, perturbed angular correlation measurements and site preference

The quadrupolar hyperfine interactions of in-diffused (111)In -> (111)Cd probes in polycrystalline isostructural Zr(4)Al(3) and Hf(4)Al(3) samples containing small admixtures of the phases (Zr/Hf)(3)Al(2) were investigated. A strong preference of (111)In solutes for the contaminant (Zr/Hf)(3)Al(2) minority phases was observed. Detailed calculations of the electric field gradient (EFG) at the Cd nucleus using the full-potential augmented plane wave + local orbital formalism allowed us to assign the observed EFG fractions to the various lattice sites in the (Zr/Hf)(3)Al(2) compounds and to understand the preferential site occupation of the minority phases by the (111)In atoms. The effects of the size of the supercell and relaxation around the oversized In and Cd probe atoms were investigated in detail.

Electronic, vibrational and related properties of group IV metal oxides by ab initio calculations

We present our theoretical results for the structural, electronic, vibrational and optical properties of MO(2) (M = Sn, Zr, Hf and Ti) obtained by first-principles calculations. Relativistic effects are demonstrated to be important for a realistic description of the detailed structure of the electronic frequency-dependent dielectric function, as well as of the carrier effective masses. Based on our results, we found that the main contribution of the high values calculated for the oxides dielectric constants arises from the vibrational properties of these oxides, and the vibrational static dielectric constant values diminish with increasing pressure. (c) 2008 Elsevier B.V. All rights reserved.

Ab initio study of the electronic and optical properties of sillimanite (Al(2)SiO(5)) crystal

Ab initio calculations based on the density functional theory (DFT) are used to investigate the electronic and optical properties of sillimanite. The geometrical parameters of the unit cell, which contain 32 atoms, have been fully optimized and are in good agreement with the experimental data. The electronic structure shows that sillimanite has an indirect band gap of 5.18 eV. The complex dielectric function and optical constants, such as extinction coefficient, refractive index, reflectivity and energy-loss spectrum, are calculated. The optical properties of sillimanite are discussed based on the band structure calculations. It is shown that the O-2p states and Al-3s, Si-3s states play the major role in optical transitions as initial and final states, respectively. (C) 2011 Elsevier B.V. All rights reserved.

Formation and decomposition of N-alkyinaphthalimides: experimental evidences and ab initio description of the reaction pathways

The kinetics of hydrolysis of 1,8-N-butyl-naphthalimide (1,8-NBN) to 1,8-N-butyl-naphthalamide (1,8-NBAmide) and of 2,3-N-butyl-naphthalimide (2,3-NBN) to 2,3-N-butyl-naphthalamide (2,3-NBAmide), as well as the formation of the respective anhydrides from the amides were investigated in a wide acidity range. 1,8-NBN equilibrates with 1,8-NBAmide in mild alkali. Under the same conditions 2,3-NBN quantitatively yields 2,3-NBAmide. Over a wide range of acidities the reactions of the 1,8- and 2,3-N-butyl-naphthalamides (or imides) yield similar products but with widely different rates and at distinct pH`s. Anhydride formation in acid was demonstrated for 1,8-NBAmide. The reactions mechanisms were rationalized in the manifold pathways of ab initio calculations. The differences in rates and pH ranges in the reactions of the 1,8- and 2,3-N-butyl-naphthalamides were attributed to differences in the stability of the tetrahedral intermediates in alkali as well as the relative stabilities of the five and six-membered ring intermediates. The rate of carboxylic acid assisted 1,8-N-Butyl-naphthalamide hydrolysis is one of the largest described for amide hydrolysis models. Copyright (C) 2010 John Wiley & Sons, Ltd.

Crystal and molecular structures of three 2-sulphur-substituted cyclohexanones studied by X-ray crystallography and by ab initio molecular orbital calculations

The conformational features of three 2-sulphur-substituted cyclohexanone derivatives, which differ in the number of sulphur-bound oxygen atoms, i.e. zero (I), one (II) and two (III), were investigated by single crystal X-ray crystallography and geometry optimized structures determined using Hartree-Fock method. In each of (I)-(III) an intramolecular S center dot center dot center dot O(carbonyl) interaction is found with the magnitude correlated with the oxidation state of the sulphur atom, i.e. 2.838(3) angstrom in (I) to 2.924(2) angstrom in (II) to 3.0973(18) angstrom in (III). There is an inverse relationship between the strength of this interaction and the magnitude of the carbonyl bond. The supramolecular aggregation patterns are primarily determined by C-H center dot center dot center dot O contacts and are similarly influenced by the number of oxygen atoms in the molecular structures. Thus, a supramolecular chain is found in the crystal structure of (I). With an additional oxygen atom available to participate in C-H center dot center dot center dot O interactions, as in (II), a two-dimensional array is found. Finally, a three-dimensional network is found for (III). Despite there being differences in conformations between the experimental structures and those calculated in the gas-phase, the S center dot center dot center dot O interactions persist. The presence of intermolecular C-H center dot center dot center dot O interactions involving the cyclohexanone-carbonyl group in the solid-state, disrupts the stabilising intramolecular C-H center dot center dot center dot O interaction in the energetically-favoured conformation. (I): C(12)H(13)NO(3)S, triclinic space group P (1) over bar with a = 5.392(3) angstrom b = 10.731(6) angstrom, c = 11.075(6) angstrom, alpha = 113.424(4)degrees, beta = 94.167(9)degrees, gamma = 98.444(6)degrees, V = 575.5(6) angstrom(3), Z = 2, R(1) = 0.052; (II): C(12)H(13)NO(4)S, monoclinic P2(1)/n, a = 7.3506(15) angstrom, b = 6.7814(14) angstrom, c = 23.479(5) angstrom, beta = 92.94(3)degrees, V = 1168.8(4) angstrom(3), Z = 4, R(1) = 0.046; (III): C(12)H(13)NO(5)S, monoclinic P2(1)/c, a = 5.5491(11) angstrom, b = 24.146(3) angstrom, c = 11.124(3) angstrom, beta = 114.590(10)degrees, V = 1355.3(5) angstrom(3), Z = 4, R(1) = 0.051.

Ab initio study of SO2 molecules interacting with pristine and transition metal covered fullerenes as a possible route for nanofilters

In this work, a systematic study of SO2 molecules interacting with pristine and transition metal (TM) covered C-60 is presented by means of first principles calculations. It is observed that the SO2 molecule interacts weakly with the pristine C-60 fullerene, although the resulting interaction is largely increased when the C-60 structure is covered with Fe, Mn, or Ti atoms and the SO2 Molecules are bounded through the TM atoms. The number of bounded SO2 molecules per TM atoms, in addition to the elevated binding energies per molecules, allows us to conclude that such composites can be used as a template for efficient devices to remove SO2 molecules or, alternatively, as SO2 gas sensor.

Hydrogen adsorption on boron doped graphene: an ab initio study

(i) The electronic and structural properties of boron doped graphene sheets, and (ii) the chemisorption processes of hydrogen adatoms on the boron doped graphene sheets have been examined by ab initio total energy calculations. In (i) we find that the structural deformations are very localized around the boron substitutional sites, and in accordance with previous studies (Endo et al 2001 J. Appl. Phys. 90 5670) there is an increase of the electronic density of states near the Fermi level. Our simulated scanning tunneling microscope (STM) images, for occupied states, indicate the formation of bright (triangular) spots lying on the substitutional boron (center) and nearest-neighbor carbon (edge) sites. Those STM images are attributed to the increase of the density of states within an energy interval of 0.5 eV below the Fermi level. For a boron concentration of similar to 2.4%, we find that two boron atoms lying on the opposite sites of the same hexagonal ring (B1-B2 configuration) represents the energetically most stable configuration, which is in contrast with previous theoretical findings. Having determined the energetically most stable configuration for substitutional boron atoms on graphene sheets, we next considered the hydrogen adsorption process as a function of the boron concentration, (ii). Our calculated binding energies indicate that the C-H bonds are strengthened near boron substitutional sites. Indeed, the binding energy of hydrogen adatoms forming a dimer-like structure on the boron doped B1-B2 graphene sheet is higher than the binding energy of an isolated H(2) molecule. Since the formation of the H dimer-like structure may represent the initial stage of the hydrogen clustering process on graphene sheets, we can infer that the formation of H clusters is quite likely not only on clean graphene sheets, which is in consonance with previous studies (Hornekaer et al 2006 Phys. Rev. Lett. 97 186102), but also on B1-B2 boron doped graphene sheets. However, for a low concentration of boron atoms, the formation of H dimer structures is not expected to occur near a single substitutional boron site. That is, the formation (or not) of H clusters on graphene sheets can be tuned by the concentration of substitutional boron atoms.

Ab initio calculation of the BCC Fe-Al-Mo (Iron-Aluminum-Molybdenum) phase diagram: Implications for the nature of the tau(2) phase

The metastable phase diagram of the BCC-based ordering equilibria in the Fe-Al-Mo system has been calculated via a truncated cluster expansion, through the combination of Full-Potential-Linear augmented Plane Wave (FP-LAPW) electronic structure calculations and of Cluster Variation Method (CVM) thermodynamic calculations in the irregular tetrahedron approximation. Four isothermal sections at 1750 K, 2000 K, 2250 K and 2500 K are calculated and correlated with recently published experimental data on the system. The results confirm that the critical temperature for the order-disorder equilibrium between Fe(3)Al-D0(3) and FeAl-B2 is increased by Mo additions, while the critical temperature for the FeAl-B2/A2 equilibrium is kept approximately invariant with increasing Mo contents. The stabilization of the Al-rich A2 phase in equilibrium with overstoichiometric B2-(Fe,Mo)Al is also consistent with the attribution of the A2 structure to the tau(2) phase, stable at high temperatures in overstoichiometric B2-FeAl. (C) 2009 Elsevier Ltd. All rights reserved.

Large Changes of Static Electric Properties Induced by Hydrogen Bonding: An ab Initio Study of Linear HCN Oligomers

We report the partitioning of the interaction-induced static electronic dipole (hyper)polarizabilities for linear hydrogen cyanide complexes into contributions arising from various interaction energy terms. We analyzed the nonadditivities of the studied properties and used these data to predict the electric properties of an infinite chain. The interaction-induced static electric dipole properties and their nonadditivities were analyzed using an approach based on numerical differentiation of the interaction energy components estimated in an external electric field. These were obtained using the hybrid variational-perturbational interaction energy decomposition scheme, augmented with coupled-cluster calculations, with singles, doubles, and noniterative triples. Our results indicate that the interaction-induced dipole moments and polarizabilities are primarily electrostatic in nature; however, the composition of the interaction hyperpolarizabilities is much more complex. The overlap effects substantially quench the contributions due to electrostatic interactions, and therefore, the major components are due to the induction and exchange induction terms, as well as the intramolecular electron-correlation corrections. A particularly intriguing observation is that the interaction first hyperpolarizability in the studied systems not only is much larger than the corresponding sum of monomer properties, but also has the opposite sign. We show that this effect can be viewed as a direct consequence of hydrogen-bonding interactions that lead to a decrease of the hyperpolarizability of the proton acceptor and an increase of the hyperpolarizability of the proton donor. In the case of the first hyperpolarizability, we also observed the largest nonadditivity of interaction properties (nearly 17%) which further enhances the effects of pairwise interactions.

Electronic and optical properties of grossular garnet (Ca(3)Al(2)Si(3)O(12)): An ab initio study

The electronic and optical properties of grossular garnet are investigated using density functional theory (DFT) within generalized gradient approximation (GGA). The calculated lattice parameters are in good agreement with the experiment data. The electronic structure shows that grossular has a direct band gap of 5.22 eV. The dielectric functions, reflective index, extinction coefficient, reflectivity and energy-loss spectrum are calculated. The optical properties of grossular are discussed based on the band structure calculations. The O 2p states and Si 3s play a major role in these optical transitions as initial and final states, respectively. The absorption spectrum is localized in the ultraviolet range between 30 and 250 nm. Finally, we concluded that pure grossular crystal does not absorb radiation in the visible range. (c) 2009 Elsevier B.V. All rights reserved.

Ab Initio Analysis of Monomers and Dimers of Trialkylphosphine Oxides: Structural and Thermodynamic Stability

Structural and thermodynamic stabilities of monomers and dimers of trialkylphosphine oxides (TRPO) were Studied using quantum chemistry calculations. Density functional theory calculations were carried Out and the structures Of four TRPO have been determined: TMPO (methyl; R = CH(3)), TEPO (ethyl; R = CH(3)CH(2)), TBPO (n-butyl; R = CH(3)(CH(2))(3)), and TOPO (n-octyl; R = CH(3)(CH(2))(7)). TRPO homodimers were investigated considering two isomeric possibilities for each dimer. Relative binding energies and the enthalpic and entropic contributions to the Gibbs free energy were Calculated for all dimers. The formation of dimers from the individual monomeric TRPO species as a function of temperature was also analyzed. (C) 2008 Wiley Periodicals, Inc. Int J Quantum Chem 109: 250-258, 2009

Ab initio study of the EFG at the N sites in imidazole

We study the nuclear quadrupole interaction at the nitrogen sites in the molecular and crystalline phases of the imidazole compound. We use PAW which is a state-of-the-art method to calculate the electronic structure and electric field gradient at the nucleus in the framework of the density functional theory. The quadrupole frequencies at both imino and amino N sites are in excellent agreement with measurements. This is the first time that the electric field gradient at crystalline imidazole is correctly treated by an ab initio theoretical approach.

The role of carbon impurities on the Si(001)-c(4 x 4) surface reconstruction: Theoretical calculations

In this work we employ the state-of-the-art pseudopotential method, within a generalized gradient approximation to the density functional theory, combined with a recently developed method for the calculation of HREELS spectra to study a series of different proposed models for carbon incorporation on the silicon (001) surface. A fully discussion on the geometry, energetics and specially the comparison between experimental and theoretical STM images and electron energy loss spectra indicate that the Si(100)-c(4 x 4) is probably induced by Si-C surface dinners, in agreement with recent experimental findings. (C) 2009 Elsevier B.V. All rights reserved.