Defect study of SnO2 nanostructures by cathodoluminescence analysis: Application to nanowires

Defects in SnO2 nanowires have been studied by cathodoluminescence, and the obtained spectra have been compared with those measured on SnO2 nanocrystals of different sizes in order to reveal information about point defects not determined by other characterization techniques. Dependence of the luminescence bands on the thermal treatment temperatures and pre-treatment conditions have been determined pointing out their possible relation, due to the used treatment conditions, with the oxygen vacancy concentration. To explain these cathodoluminescence spectra and their behavior, a model based on first-principles calculations of the surface oxygen vacancies in the different crystallographic directions is proposed for corroborating the existence of surface state bands localized at energy values compatible with the found cathodoluminescence bands and with the gas sensing mechanisms. CL bands centered at 1.90 and 2.20 eV are attributed to the surface oxygen vacancies 100° coordinated with tin atoms, whereas CL bands centered at 2.37 and 2.75 eV are related to the surface oxygen vacancies 130° coordinated. This combined process of cathodoluminescence and ab initio calculations is shown to be a powerful tool for nanowire defect analysis.

Vortices in atomic Bose-Einstein condensates in the large-gas-parameter region

In this work we compare the results of the Gross-Pitaevskii and modified Gross-Pitaevskii equations with ab initio variational Monte Carlo calculations for Bose-Einstein condensates of atoms in axially symmetric traps. We examine both the ground state and excited states having a vortex line along the z axis at high values of the gas parameter and demonstrate an excellent agreement between the modified Gross-Pitaevskii and ab initio Monte Carlo methods, both for the ground and vortex states.

Relativistic mean-field interaction with density-dependent meson-nucleon vertices based on microscopical calculations

Although ab initio calculations of relativistic Brueckner theory lead to large scalar isovector fields in nuclear matter, at present, successful versions of covariant density functional theory neglect the interactions in this channel. A new high-precision density functional DD-MEδ is presented which includes four mesons, σ, ω, δ, and ρ, with density-dependent meson-nucleon couplings. It is based to a large extent on microscopic ab initiocalculations in nuclear matter. Only four of its parameters are determined by adjusting to binding energies and charge radii of finite nuclei. The other parameters, in particular the density dependence of the meson-nucleon vertices, are adjusted to nonrelativistic and relativistic Brueckner calculations of symmetric and asymmetric nuclear matter. The isovector effective mass mp*−mn* derived from relativistic Brueckner theory is used to determine the coupling strength of the δ meson and its density dependence.

TCRep 3D: an automated in silico approach to study the structural properties of TCR repertoires.

TCRep 3D is an automated systematic approach for TCR-peptide-MHC class I structure prediction, based on homology and ab initio modeling. It has been considerably generalized from former studies to be applicable to large repertoires of TCR. First, the location of the complementary determining regions of the target sequences are automatically identified by a sequence alignment strategy against a database of TCR Vα and Vβ chains. A structure-based alignment ensures automated identification of CDR3 loops. The CDR are then modeled in the environment of the complex, in an ab initio approach based on a simulated annealing protocol. During this step, dihedral restraints are applied to drive the CDR1 and CDR2 loops towards their canonical conformations, described by Al-Lazikani et. al. We developed a new automated algorithm that determines additional restraints to iteratively converge towards TCR conformations making frequent hydrogen bonds with the pMHC. We demonstrated that our approach outperforms popular scoring methods (Anolea, Dope and Modeller) in predicting relevant CDR conformations. Finally, this modeling approach has been successfully applied to experimentally determined sequences of TCR that recognize the NY-ESO-1 cancer testis antigen. This analysis revealed a mechanism of selection of TCR through the presence of a single conserved amino acid in all CDR3β sequences. The important structural modifications predicted in silico and the associated dramatic loss of experimental binding affinity upon mutation of this amino acid show the good correspondence between the predicted structures and their biological activities. To our knowledge, this is the first systematic approach that was developed for large TCR repertoire structural modeling.

Nonempirical cluster-model study of the chemisorption of atomic hydrogen on the (111) surface of diamondlike crystals

The interaction of atomic hydrogen with C4H9, Si4H9, and Ge4H9 model clusters has been studied using all-electron and pseudopotential ab initio Hartree-Fock computations with basis sets of increasing flexibility. The results show that the effect of polarization functions is important in order to reproduce the experimental findings, but their inclusion only for the atoms directly involved in the chemisorption bond is usually sufficient. For the systems H-C4H9 and H-Si4H9 all-electron and pseudopotential results are in excellent agreement when basis sets of comparable quality are used. Besides, semiempirical modified-neglect-of-differential-overlap computations provide quite reliable results both for diamond and silicon and have been used to investigate larger model clusters. The results confirm the local nature of chemisorption and further justify the use of minimal X4H9 model clusters.

Evidence for oxygen-island formation on Al(111): Cluster-model theory and x-ray photoelectron spectroscopy

The O 1s x-ray photoelectron spectroscopy spectrum for Al(111)/O at 300 K shows two components whose behavior as a function of time and variation of detection angle are consistent with either (a) a surface species represented by the higher binding-energy (BE) component and a subsurface species represented by the lower BE component, or (b) small close-packed oxygen islands with the interior atoms represented by the lower BE component and the perimeter atoms by the higher BE component. We have modeled both situations using ab initio Hartree-Fock wave functions for clusters of Al and O atoms. For an O atom in a threefold site, it was found that a below-surface position gave a higher O 1s BE than an above-surface position, incompatible with interpretation (a). This change in the O 1s BE could arise because the bond for O to Al may have a more covalent character when the O is below the surface than when it is above the surface. We present evidence consistent with this view. An O adatom island with all the O atoms in threefold sites gives calculated O 1s BE's which are significantly higher for the perimeter O atoms. Further, the results for an isolated O island without the Al substrate present also give higher BE¿s for the perimeter atoms. Both these results are consistent with interpretation (b). Published scanning-tunneling-microscopy data supports the suggestion that the chemisorbed state consists of small, close-packed islands, whereas the presence of two vibrational modes in high-resolution electron-energy-loss spectroscopy data has been interpreted as representing surface and subsurface oxygen atoms. In light of the present results, we suggest that a vibrational interpretation in terms of interior and perimeter adatoms should be considered.

Evidence for two different bonding mechanisms of Al on Si(111)

By means of the ab initio cluster-model approach, we present theoretical evidence for two different mechanisms of bonding of atomic Al to Si(111). On the atop site (T1) the interaction of atomic Al to Si(111) is characteristic of an ionic bond whereas interaction above the threefold eclipsed site (T4) leads to the formation of a typical covalent bond. Moreover, both sites have a similar interaction energy if electronic correlation effects are included. While the conclusions regarding the nature of the chemisorption bond in the two sites do not depend either on the cluster-model size, the kind of embedding hydrogen atoms used, or the quality of the wave function (Hartree-Fock or configuration interaction), the chemisorption energy depends strongly on the wave function used. In fact, inclusion of correlation energy is necessary to properly describe the interaction energies.

Electronic structure and properties of AlN

The electronic structure of the wurtzite-type phase of aluminum nitride has been investigated by means of periodic ab initio Hartree-Fock calculations. The binding energy, lattice parameters (a,c), and the internal coordinate (u) have been calculated. All structural parameters are in excellent agreement with the experimental data. The electronic structure and bonding in AlN are analyzed by means of density-of-states projections and electron-density maps. The calculated values of the bulk modulus, its pressure derivative, the optical-phonon frequencies at the center of the Brillouin zone, and the full set of elastic constants are in good agreement with the experimental data.

Extent and limitations of density functional theory in describing magnetic systems

The performance of density-functional theory to solve the exact, nonrelativistic, many-electron problem for magnetic systems has been explored in a new implementation imposing space and spin symmetry constraints, as in ab initio wave function theory. Calculations on selected systems representative of organic diradicals, molecular magnets and antiferromagnetic solids carried out with and without these constraints lead to contradictory results, which provide numerical illustration on this usually obviated problem. It is concluded that the present exchange-correlation functionals provide reasonable numerical results although for the wrong physical reasons, thus evidencing the need for continued search for more accurate expressions.

Absence of collective effects in Heisenberg systems with localized magnetic moments

Existence of collective effects in magnetic coupling in ionic solids is studied by mapping spin eigenstates of the Heisenberg and exact nonrelativistic Hamiltonians on cluster models representing KNiF3, K2NiF4, NiO, and La2CuO4. Ab initio techniques are used to estimate the Heisenberg constant J. For clusters with two magnetic centers, the values obtained are about the same for models having more magnetic centers. The absence of collective effects in J strongly suggests that magnetic interactions in this kind of ionic solids are genuinely local and entangle only the two magnetic centers involved.

Local character of magnetic coupling in ionic solids

Magnetic interactions in ionic solids are studied using parameter-free methods designed to provide accurate energy differences associated with quantum states defining the Heisenberg constant J. For a series of ionic solids including KNiF3, K2NiF4, KCuF3, K2CuF4, and high- Tc parent compound La2CuO4, the J experimental value is quantitatively reproduced. This result has fundamental implications because J values have been calculated from a finite cluster model whereas experiments refer to infinite solids. The present study permits us to firmly establish that in these wide-gap insulators, J is determined from strongly local electronic interactions involving two magnetic centers only thus providing an ab initio support to commonly used model Hamiltonians.

Magnetic coupling in the weac ferromagnet CuF2

CuF2 is known to be an antiferromagnetic compound with a weak ferromagnetism due to the anisotropy of its monoclinic unit cell (Dzialoshinsky-Moriya mechanism). We investigate the magnetic ordering of this compound by means of ab initio periodic unrestricted Hartree-Fock calculations and by cluster calculations which employ state-of-the-art configuration interaction expansions and modern density functional theory techniques. The combined use of periodic and cluster models permits us to firmly establish that the antiferromagnetic order arises from the coupling of one-dimensional subunits which themselves exhibit a very small ferromagnetic coupling between Cu neighbor cations. This magnetic order could be anticipated from the close correspondence between CuF2 and rutile crystal structures.

Electronic structure and magnetic interactions of the spin-chain compounds Ca2CuO3 and Sr2CuO3

The results are presented of a combined periodic and cluster model approach to the electronic structure and magnetic interactions in the spin-chain compounds Ca2CuO3 and Sr2CuO3. An extended t-J model is presented that includes in-chain and interchain hopping and magnetic interaction processes with parameters extracted from ab initio calculations. For both compounds, the in-chain magnetic interaction is found to be around -240 meV, larger than in any of the other cuprates reported in the literature. The interchain magnetic coupling is found to be weakly antiferromagnetic, -1 meV. The effective in-chain hopping parameters are estimated to be ~650 meV for both compounds, whereas the value of the interchain hopping parameter is 30 meV for Sr2CuO3 and 40 meV for Ca2CuO3, in line with the larger interchain distance in the former compound. These effective parameters are shown to be consistent with expressions recently suggested for the Néel temperature and the magnetic moments, and with relations that emerge from the t-J model Hamiltonian. Next, we investigate the physical nature of the band gap. Periodic calculations indicate that an interpretation in terms of a charge-transfer insulator is the most appropriate one, in contrast to the suggestion of a covalent correlated insulator recently reported in the literature.

Electronic structure of a neutral oxygen vacancy in SrTiO3

The electronic structure of an isolated oxygen vacancy in SrTiO3 has been investigated with a variety of ab initio quantum mechanical approaches. In particular we compared pure density functional theory (DFT) approaches with the Hartree-Fock method, and with hybrid methods where the exchange term is treated in a mixed way. Both local cluster models and periodic calculations with large supercells containing up to 80 atoms have been performed. Both diamagnetic (singlet state) and paramagnetic (triplet state) solutions have been considered. We found that the formation of an O vacancy is accompanied by the transfer of two electrons to the 3d(z2) orbitals of the two Ti atoms along the Ti-Vac-Ti axis. The two electrons are spin coupled and the ground state is diamagnetic. New states associated with the defect center appear in the gap just below the conduction band edge. The formation energy computed with respect to an isolated oxygen atom in the triplet state is 9.4 eV.

Ionic-covalent transition in titanium oxides

The nature of the chemical bond in three titanium oxides of different crystal structure and different formal oxidation state has been studied by means of the ab initio cluster-model approach. The covalent and ionic contributions to the bond have been measured from different theoretical techniques. All the analysis is consistent with an increasing of covalence in the TiO, Ti2O3, and TiO2 series as expected from chemical intuition. Moreover, the use of the ab initio cluster-model approach combined with different theoretical techniques has permitted us to quantify the degree of ionic character, showing that while TiO can approximately be described as an ionic compound, TiO2 is better viewed as a rather covalent oxide.