Showing papers by "José M. Soler published in 2006"

Planar and cagelike structures of gold clusters: Density-functional pseudopotential calculations

Abstract: We study why gold forms planar and cagelike clusters while copper and silver do not. We use density functional theory and norm-conserving pseudopotentials with and without a scalar relativistic component. For the exchange-correlation (xc) functional we use both the generalized gradient (GGA) and the local density (LDA) approximations. We find that planar ${\mathrm{Au}}_{n}$ structures, with up to $n=11$, have lower energy than the three-dimensional isomers only with scalar-relativistic pseudopotentials and the GGA. In all other calculations, with more than six or seven noble metal atoms, we obtain three-dimensional (3D) structures. However, as a general trend we find that planar structures are more favorable with the GGA than with the LDA. In the total energy balance, kinetic energy favors planar and cage structures, while xc energy favors 3D structures. As a second step, we construct cluster structures having only surface atoms with ${O}_{h}$, ${T}_{d}$, and ${I}_{h}$ symmetry. Then, assuming one valence electron per atom, we select those with $2(l+1{)}^{2}$ electrons (with $l$ integer), which correspond to the filling of a spherical electronic shell formed by nodeless one-electron wave functions. Using scalar relativistic GGA molecular dynamics at $T=600\phantom{\rule{0.3em}{0ex}}\mathrm{K}$, we show that the cagelike structures of neutral ${\mathrm{Au}}_{32}$, ${\mathrm{Au}}_{50}$, and ${\mathrm{Au}}_{162}$ are metastable. Finally, we calculate the static polarizability of the two lowest-energy isomers of ${\mathrm{Au}}_{n}$ clusters as a means to discriminate isomers with planar (or cagelike) geometry from those with compact structures. We also fit our data to a semiempirical relation for the size-dependent polarizability which involves the effective valence and kinetic energy components for the homogeneous and inhomogeneous electron densities. Analyzing that fit, we find that the dipole polarizability of gold clusters with planar and cagelike structures corresponds to the linear response of 1.56 delocalized valence electrons, suggesting a strong screening of the valence interactions due to the $d$ electrons.

Ab initio study of metal-organic framework-5 Zn 4 O ( 1 , 4 − benzenedicarboxylate ) 3 : An assessment of mechanical and spectroscopic properties

Abstract: The electronic structure of porous metal-organic framework-5 (MOF-5) of composition ${\mathrm{Zn}}_{4}\mathrm{O}(1,4\text{\ensuremath{-}}\mathrm{benzenedicarboxylate}{)}_{3}$ was investigated with an ab initio density-functional-theory method. The unit cell volume and atomic positions were optimized with the well-known local-density approximation leading to a good agreement between the experimental and theoretical equilibrium structural parameters. Single crystal elastic constants (${C}_{11}$, ${C}_{12}$, and ${C}_{44}$) were then computed at the athermal limit in order to estimate fundamental figures for technological and engineering applications. Our calculations suggest that MOF-5 behaves as a soft and ductile material with a Young's modulus of the order of Oak wood. Particular attention was also focused on the study of oxygen, and carbon $K$ XANES spectra. The differences in their shapes and energy peak positions were discussed in relation to the bonding topology and to the different calculational methods used.

Geometry and electronic structure of M -DNA ( M = Zn 2 + , Co 2 + , and Fe 2 + )

Abstract: We have investigated, by means of first principles calculations, modified forms of DNA with divalent Zn, Co, Fe cations bonded to the two helix strands of poly(dC)-poly(dG). We propose a common stable structure that is consistent with the experimental reports for Zn-DNA. In all three cases, the band gap is much narrower, and the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) bands are considerably wider than those in dry DNA. In Zn-DNA, the HOMO LUMO bands are formed purely by guanine cytosine states, respectively, with no weight in the Zn atoms. Their large width arise from an increased overlap between $\ensuremath{\pi}$ states of the bases, due to the helix deformation after the insertion of the Zn ion. Contrarily, the HOMO and LUMO bands of Co-DNA and Fe-DNA have a large weight on the metal atoms. These results offer promising perspectives for turning DNA into a conducting wire.

Dislocation formation from a surface step in semiconductors: An ab initio study

Abstract: The role of a simple surface defect, such as a step, for relaxing the stress applied to a semiconductor, has been investigated by means of large-scale first-principles calculations. Our results indicate that the step is the privileged site for initiating plasticity, with the formation and glide of 60 degrees dislocations for both tensile and compressive deformations. We have also examined the effect of surface and step termination on the plastic mechanisms.

Separating the articles of authors with the same name

Abstract: I describe a method to separate the articles of different authors with the same name. It is based on a distance between any two publications, defined in terms of the probability that they would have as many coincidences if they were drawn at random from all published documents. Articles with a given author name are then clustered according to their distance, so that all articles in a cluster belong very likely to the same author. The method has proven very useful in generating groups of papers that are then selected manually. This simplifies considerably citation analysis when the author publication lists are not available.

Magnetism of two-dimensional defects in Pd: Stacking faults, twin boundaries, and surfaces

Abstract: Careful first-principles density functional calculations reveal the importance of hexagonal versus cubic stacking of close-packed planes of Pd as far as local magnetic properties are concerned. We find that, contrary to the stable face-centered-cubic phase, which is paramagnetic, the hexagonal-close-packed phase of Pd is ferromagnetic with a magnetic moment of $0.35\phantom{\rule{0.3em}{0ex}}{\ensuremath{\mu}}_{B}∕\mathrm{atom}$. Our results show that two-dimensional defects with local hcp stacking, like twin boundaries and stacking faults, in the otherwise fcc Pd structure, increase the magnetic susceptibility. The (111) surface also increases the magnetic susceptibility and it becomes ferromagnetic in combination with an individual stacking fault or twin boundary close to it. On the contrary, we find that the (100) surface decreases the tendency to ferromagnetism. The results are consistent with the magnetic moment recently observed in small Pd nanoparticles, with a large surface area and a high concentration of two-dimensional stacking defects.

Comment on "Magnetism in Atomic-Size Palladium Contacts and Nanowires"

Abstract: A Comment on the Letter by A. Delin, E. Tosatti, and R. Weht, Phys. Rev. Lett. 92, 057201 (2004). The authors of the Letter offer a Reply.

Efficient and reliable method for the simulation of scanning tunneling images and spectra with local basis sets

Abstract: Based on Bardeen's perturbative approach to tunneling, we have found an expression for the current between tip and sample, which can be efficiently coded in order to perform fast ab initio simulations of STM images. Under the observation that the potential between the electrodes should be nearly flat at typical tunnel gaps, we have addressed the difficulty in the computation of the tunneling matrix elements by considering a vacuum region of constant potential delimited by two surfaces (each of them close to tip and sample respectively), then propagating tip and sample wave functions by means of the vacuum Green's function, to finally obtain a closed form in terms of convolutions. The current is then computed for every tip-sample relative position and for every bias voltage in one shot. The electronic structure of tip and sample is calculated at the same footing, within density functional theory, and independently. This allows us to carry out multiple simulations for a given surface with a database of different tips. We have applied this method to the Si(111)-(7x7) and Ge(111)-c(2x8) surfaces. Topographies and spectroscopic data, showing a very good agreement with experiments, are presented.

Efficient and reliable method for the simulation of scanning tunneling images and spectra with local basis sets

Abstract: Based on Bardeen's perturbative approach to tunneling, we have found an expression for the current between tip and sample, which can be efficiently coded in order to perform fast ab initio simulations of STM images. Under the observation that the potential between the electrodes should be nearly flat at typical tunnel gaps, we have addressed the difficulty in the computation of the tunneling matrix elements by considering a vacuum region of constant potential delimited by two surfaces (each of them close to tip and sample respectively), then propagating tip and sample wave functions by means of the vacuum Green's function, to finally obtain a closed form in terms of convolutions. The current is then computed for every tip-sample relative position and for every bias voltage in one shot. The electronic structure of tip and sample is calculated at the same footing, within density functional theory, and independently. This allows us to carry out multiple simulations for a given surface with a database of different tips. We have applied this method to the Si(111)-(7 x 7) and Ge(111)-c(2 x 8) surfaces. Topographies and spectroscopic data, showing a very good agreement with experiments, are presented.

Filtering a distribution simultaneously in real and Fourier space

Abstract: We present a method to filter a distribution so that it is confined within a sphere of given radius ${r}_{c}$ and, simultaneously, whose Fourier transform is optimally confined within a sphere of radius ${k}_{c}$. Our procedure may have several applications in the field of electronic structure methods, like the generation of optimized pseudopotentials and localized pseudocore charge distributions. As an example, we describe a particular application within the SIESTA method for density functional calculations, in removing the spurious rippling of the energy surface generated by the integrations in a real-space grid.

A Rational Indicator of Scientific Creativity

Abstract: A model is proposed for the creation and transmission of scientific knowledge, based on the network of citations among research articles. The model allows to assign to each article a nonnegative value for its creativity, i. e. its creation of new knowledge. If the entire publication network is truncated to the first neighbors of an article (the n references that it makes and the m citations that it receives), its creativity value becomes a simple function of n and m. After splitting the creativity of each article among its authors, the cumulative creativity of an author is then proposed as an indicator of her or his merit of research. In contrast with other merit indicators, this creativity index yields similar values for the top scientists in two very different areas (life sciences and physics), thus offering good promise for interdisciplinary analyses.