Biomedical subjects

Pablo Ordejón

Publications and source records attributed to Pablo Ordejón.

5 recordsLinked to original sources

PubMed2006

Electronic structure and charge transfer in the ternary intercalated graphite beta-KS0.25C3.

The electronic structure of the ternary intercalated graphite beta-KS(0.25)C3 is studied by means of a first-principles density functional theory approach. The nature of the partially filled bands is analyzed, and the K sublayers of the intercalate are shown to have an important contribution to the Fermi surface. This K-based contribution confers a sizable three-dimensional character to the conductivity even if considerably less than that for the related binary KC8. The electronic structure of beta-KS(0.25)C3 differs noticeably from that of the related ternary compound, KH(x)C4. The charge transfer is analyzed, and a way to evaluate it, which can be used in general for intercalated graphites, is proposed. The charge transfer per C atom in this ternary material is shown to be smaller than that in the KC8 binary compound despite a more favorable stoichiometry ratio between K and C.

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PubMed2005

Scanning tunneling microscopy and surface simulation of zinc-blende GaN(001) intrinsic 4x reconstruction: linear gallium tetramers?

Scanning tunneling microscopy images confirm electron diffraction studies that the zinc-blende GaN(001)-4x reconstruction consists of rows aligned along [110] with a spacing along [110] of 4a. Dual-bias imaging shows a 180 degree shift of the corrugation maximum position between the profiles of empty and occupied states, in agreement with surface simulations based on the 4 x 1 linear tetramer model of Neugebauer et al. [Phys. Rev. Lett. 80, 3097 (1998)]. Electronic structure calculations predict a surface band gap of 1.1 eV, close to the measured value of 1.14 eV and the previously predicted value (1.2 eV). Despite the successes of this model, high-resolution images reveal an unexpected 3x periodicity (not seen in diffraction) along the [110] row direction, indicating the need for a 4 x 3 model, and putting into question the existence of linear Ga tetramers.

Journal Article↗

PubMed2005

First-principles analyses and predictions on the reactivity of barrier layers of Ta and TaN toward organometallic precursors for deposition of copper films.

We present theoretical studies based on first-principles density functional theory calculations on the mechanisms of chemical vapor deposition of Cu-hexafluoracetylacetonato-trimethylvinylsilane (Cu(hfac)(tmvs)) on tantalum surfaces. This process has been used in the past to grow copper films via a disproportionation reaction and was found to exhibit adhesion problems. We show that the Ta surfaces are highly reactive and that the organic ligands in a copper precursor would undergo spontaneous decomposition upon contact with the Ta substrates. This may lead to contamination of the metal surfaces caused by the formation of carbide, fluoride, oxide species, or other fragments of the copper precursor on the barrier layer. We propose a practical solution for these adhesion problems caused by the CVD process by passivating the metal surfaces with N(2) to reduce their activity toward the precursor. Our extensive first-principles molecular dynamics simulations under typical deposition conditions predict that, for properly passivated TaN surfaces, only the copper atoms are firmly adsorbed on the surface, with loose Cu-ligand bonds. The ligands are sufficiently stable on these passivated surfaces, remaining slightly above the surface due to the repulsion between the electron-rich N-layer and the electron-rich ligand groups, and subsequently liberated upon the disproportionation reaction.

Journal Article↗

PubMed2003

Modulation of the NO trans effect in heme proteins: implications for the activation of soluble guanylate cyclase.

The binding of NO to the iron heme in guanylate cyclase and other heme proteins induces the cleavage of the proximal histidine bonded to the metal. In this study we assess by means of density functional theory (DFT) electronic structure calculations the role of H-bonding to histidine in the modulation of this effect. We have considered in the first place a model of the isolated active site coordinated with imidazole and imidazolate to mimic the effects of a very strong H-bond. We have also investigated four selected ferrous heme proteins with different proximal histidine environments: the O(2) sensing FixL, horseradish peroxidase C, and the alpha and beta subunits of human hemoglobin. Our results indicate that polarization and charge transfer effects associated with H-bonding to the proximal histidine play a fundamental role in the modulation of the NO trans effect in heme proteins. We also find computational evidence suggesting that protein structural constraints may affect significantly the cleavage of the Fe-His bond.

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PubMed2003

TranSIESTA: a spice for molecular electronics.

Our recently developed method, TranSIESTA, enables modelling of molecular electronic devices under operation conditions. The method is based on density functional theory, and calculates the self-consistent electronic structure of a nanostructure coupled to three-dimensional electrodes with different electrochemical potentials. It uses a full atomistic ab initio description of both the electrodes and the nanoscale device. The calculations reveal information about the scattering states, transmission coefficients, electron current, and non-equilibrium forces in the systems. In this paper we use the method to investigate the electrical properties of three ring phenyl-ethynylene oligomers (OPE). We present results for the electrical effect of side groups and molecular conformations of the molecules. The calculations indicate that molecular switching and negative differential conductance (NDC) are related to rotations of the middle phenyl ring.

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