CO adsorption on Pt induced Ge nanowires

Using density functional theory, we investigate the possible adsorption sites of CO molecules on the recently discovered Pt induced Ge nanowires on Ge(001). Calculated STM images are compared to experimental STM images to identify the experimentally observed adsorption sites. The CO molecules are found to adsorb preferably onto the Pt atoms between the Ge nanowire dimer segments. This adsorption site places the CO in between two nanowire dimers, pushing them outward, blocking the nearest equivalent adsorption sites. This explains the observed long-range repulsive interaction between CO molecules on these Pt induced nanowires.Comment: 12 pages, 10 figure

Tunable Hydrogen Storage in Magnesium - Transition Metal Compounds

Magnesium dihydride (\mgh) stores 7.7 weight % hydrogen, but it suffers from a high thermodynamic stability and slow (de)hydrogenation kinetics. Alloying Mg with lightweight transition metals (TM = Sc, Ti, V, Cr) aims at improving the thermodynamic and kinetic properties. We study the structure and stability of Mg$_x$TM$_{1-x}$H$_2$ compounds, $x=[0$-1], by first-principles calculations at the level of density functional theory. We find that the experimentally observed sharp decrease in hydrogenation rates for $x\gtrsim0.8$ correlates with a phase transition of Mg$_x$TM$_{1-x}$H$_2$ from a fluorite to a rutile phase. The stability of these compounds decreases along the series Sc, Ti, V, Cr. Varying the transition metal (TM) and the composition $x$, the formation enthalpy of Mg$_x$TM$_{1-x}$H$_2$ can be tuned over the substantial range 0-2 eV/f.u. Assuming however that the alloy Mg$_x$TM$_{1-x}$ does not decompose upon dehydrogenation, the enthalpy associated with reversible hydrogenation of compounds with a high magnesium content ($x=0.75$) is close to that of pure Mg.Comment: 8 pages, 5 figure

Structural studies of phosphorus induced dimers on Si(001)

Renewed focus on the P-Si system due to its potential application in quantum computing and self-directed growth of molecular wires, has led us to study structural changes induced by P upon placement on Si(001)-$p(2\times 1)$. Using first-principles density functional theory (DFT) based pseudopotential method, we have performed calculations for P-Si(001) system, starting from an isolated P atom on the surface, and systematically increasing the coverage up to a full monolayer. An isolated P atom can favorably be placed on an {\bf M} site between two atoms of adjacent Si dimers belonging to the same Si dimer row. But being incorporated in the surface is even more energetically beneficial due to the participation of the {\bf M} site as a receptor for the ejected Si. Our calculations show that up to 1/8 monolayer coverage, hetero-dimer structure resulting from replacement of surface Si atoms with P is energetically favorable. Recently observed zig-zag features in STM are found to be consistent with this replacement process. As coverage increases, the hetero-dimers give way to P-P ortho-dimers on the Si dimer rows. This behavior is similar to that of Si-Si d-dimers but are to be contrasted with the Al-Al dimers, which are found between adjacent Si dimers rows and in a para-dimer arrangement. Unlike Al-Si system P-Si does not show any para to ortho transition. For both systems, the surface reconstruction is lifted at about one monolayer coverage. These calculations help us in understanding the experimental data obtained using scanning tunneling microscope.Comment: To appear in PR

Stability of conductance oscillations in monatomic sodium wires

We study the stability of conductance oscillations in monatomic sodium wires with respect to structural variations. The geometry, the electronic structure and the electronic potential of sodium wires suspended between two sodium electrodes are obtained from self-consistent density functional theory calculations. The conductance is calculated within the framework of the Landauer-B\"utttiker formalism, using the mode-matching technique as formulated recently in a real-space finite-difference scheme [Phys. Rev. B \textbf{70}, 195402 (2004)]. We find a regular even-odd conductance oscillation as a function of the wire length, where wires comprising an odd number of atoms have a conductance close to the quantum unit $G_0=e^2/\pi\hbar$, and even-numbered wires have a lower conductance. The conductance of odd-numbered wires is stable with respect to geometry changes in the wire or in the contacts between the wire and the electrodes; the conductance of even-numbered wires is more sensitive. Geometry changes affect the spacing and widths of the wire resonances. In the case of odd-numbered wires the transmission is on-resonance, and hardly affected by the resonance shapes, whereas for even-numbered wires the transmission is off-resonance and sensitive to the resonance shapes. Predicting the amplitude of the conductance oscillation requires a first-principles calculation based upon a realistic structure of the wire and the leads. A simple tight-binding model is introduced to clarify these results.Comment: 16 pages, 20 figure

Real space finite difference method for conductance calculations

We present a general method for calculating coherent electronic transport in quantum wires and tunnel junctions. It is based upon a real space high order finite difference representation of the single particle Hamiltonian and wave functions. Landauer's formula is used to express the conductance as a scattering problem. Dividing space into a scattering region and left and right ideal electrode regions, this problem is solved by wave function matching (WFM) in the boundary zones connecting these regions. The method is tested on a model tunnel junction and applied to sodium atomic wires. In particular, we show that using a high order finite difference approximation of the kinetic energy operator leads to a high accuracy at moderate computational costs.Comment: 13 pages, 10 figure

First principles modelling of magnesium titanium hydrides

Mixing Mg with Ti leads to a hydride Mg(x)Ti(1-x)H2 with markedly improved (de)hydrogenation properties for x < 0.8, as compared to MgH2. Optically, thin films of Mg(x)Ti(1-x)H2 have a black appearance, which is remarkable for a hydride material. In this paper we study the structure and stability of Mg(x)Ti(1-x)H2, x= 0-1 by first-principles calculations at the level of density functional theory. We give evidence for a fluorite to rutile phase transition at a critical composition x(c)= 0.8-0.9, which correlates with the experimentally observed sharp decrease in (de)hydrogenation rates at this composition. The densities of states of Mg(x)Ti(1-x)H2 have a peak at the Fermi level, composed of Ti d states. Disorder in the positions of the Ti atoms easily destroys the metallic plasma, however, which suppresses the optical reflection. Interband transitions result in a featureless optical absorption over a large energy range, causing the black appearance of Mg(x)Ti(1-x)H2.Comment: 22 pages, 9 figures, 4 table

Identification of a methylase required for 2-methylhopanoid production and implications for the interpretation of sedimentary hopanes

The rise of atmospheric oxygen has driven environmental change and biological evolution throughout much of Earth’s history and was enabled by the evolution of oxygenic photosynthesis in the cyanobacteria. Dating this metabolic innovation using inorganic proxies from sedimentary rocks has been difficult and one important approach has been to study the distributions of fossil lipids, such as steranes and 2-methylhopanes, as biomarkers for this process. 2-methylhopanes arise from degradation of 2-methylbacteriohopanepolyols (2-MeBHPs), lipids thought to be synthesized primarily by cyanobacteria. The discovery that 2-MeBHPs are produced by an anoxygenic phototroph, however, challenged both their taxonomic link with cyanobacteria and their functional link with oxygenic photosynthesis. Here, we identify a radical SAM methylase encoded by the hpnP gene that is required for methylation at the C-2 position in hopanoids. This gene is found in several, but not all, cyanobacteria and also in α -proteobacteria and acidobacteria. Thus, one cannot extrapolate from the presence of 2-methylhopanes alone, in modern environments or ancient sedimentary rocks, to a particular taxonomic group or metabolism. To understand the origin of this gene, we reconstructed the evolutionary history of HpnP. HpnP proteins from cyanobacteria, Methylobacterium species, and other α-proteobacteria form distinct phylogenetic clusters, but the branching order of these clades could not be confidently resolved. Hence,it is unclear whether HpnP, and 2-methylhopanoids, originated first in the cyanobacteria. In summary, existing evidence does not support the use of 2-methylhopanes as biomarkers for oxygenic photosynthesis

Ab-initio calculation of the electronic and optical excitations in polythiophene: effects of intra- and interchain screening

We present an calculation of the electronic and optical excitations of an isolated polythiophene chain as well as of bulk polythiophene. We use the GW approximation for the electronic self-energy and include excitonic effects by solving the electron-hole Bethe-Salpeter equation. The inclusion of interchain screening in the case of bulk polythiophene drastically reduces both the quasi-particle band gap and the exciton binding energies, but the optical gap is hardly affected. This finding is relevant for conjugated polymers in general.Comment: 4 pages, 1 figur

Ab-initio prediction of the electronic and optical excitations in polythiophene: isolated chains versus bulk polymer

We calculate the electronic and optical excitations of polythiophene using the GW approximation for the electronic self-energy, and include excitonic effects by solving the electron-hole Bethe-Salpeter equation. Two different situations are studied: excitations on isolated chains and excitations on chains in crystalline polythiophene. The dielectric tensor for the crystalline situation is obtained by modeling the polymer chains as polarizable line objects, with a long-wavelength polarizability tensor obtained from the ab-initio polarizability function of the isolated chain. With this model dielectric tensor we construct a screened interaction for the crystalline case, including both intra- and interchain screening. In the crystalline situation both the quasi-particle band gap and the exciton binding energies are drastically reduced in comparison with the isolated chain. However, the optical gap is hardly affected. We expect this result to be relevant for conjugated polymers in general.Comment: 15 pages including 4 figures; to appear in Phys. Rev. B, 6/15/200