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The Born-Oppenheimer approximation is the keystone for molecular dynamics simulations of radiation damage processes; however, actual materials response involves nonadiabatic energy exchange between nuclei and electrons. In this work, time dependent density functional theory is used to calculate the electronic excitations produced by energetic protons in Al. We study the influence of these electronic excitations on the interatomic forces and find that they differ substantially from the adiabatic case, revealing a nontrivial connection between electronic and nuclear stopping that is absent in the adiabatic case. These results unveil new effects in the early stages of radiation damage cascades. © 2012 American Physical Society., A. A. C. acknowledges that part of this work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344. D. S. P. acknowledges support from the Spanish MICINN (Project No. 2010-19609-C02-02). A.C. acknowledges support from the Center for Materials at Irradiation and Mechanical Extremes, an Energy Frontier Research Center funded by the U.S. Department of Energy (Award No. 2008LANL1026) at Los Alamos National Laboratory, and from the Laboratory Directed Research and Development Program. Wellcome Trust for funding a sabbatical leave

SIESTA was developed as an approach to compute the electronic properties and perform atomistic simulations of complex materials from first principles. Very large systems, with an unprecedented number of atoms, can be studied while keeping the computational cost at a reasonable level. The SIESTA code is freely available for the academic community (http://www.uam.es/siesta), and this has made it a widely used tool for the study of materials. It has been applied to a large variety of systems including surfaces, adsorbates, nanotubes, nanoclusters, biological molecules, amorphous semiconductors, ferroelectric films, low-dimensional metals, etc. Here we present a thorough review of the applications in materials science to date.

Using density-functional calculations, we study the effect of sp 3-type defects created by different covalent functionalizations on the electronic and magnetic properties of graphene. We find that the induced magnetic properties are universal, in the sense that they are largely independent of the particular adsorbates considered. When a weakly polar single covalent bond is established with the layer, a local spin moment of 1.0 μ B always appears in graphene. This effect is similar to that of H adsorption, which saturates one p z orbital in the carbon layer. The magnetic couplings between the adsorbates show a strong dependence on the graphene sublattice of chemisorption. Molecules adsorbed at the same sublattice couple ferromagnetically, with an exchange interaction that decays very slowly with distance, while no magnetism is found for adsorbates at opposite sublattices. Similar magnetic properties are obtained if several p z orbitals are saturated simultaneously by the adsorption of a large molecule. These results might open new routes to engineering the magnetic properties of graphene derivatives by chemical means. © IOP Publishing Ltd and Deutsche Physikalische Gesellschaft., We acknowledge support from Basque Departamento de Educación and the UPV/EHU (grant no. IT-366-07), the Spanish Ministerio de Educación y Ciencia (grant no. FIS2010-19609-CO2-02) and the ETORTEK program funded by the Basque Departamento de Industria and the Diputación Foral de Gipuzkoa. EJGS acknowledges support from the CSIC JAE-predoc program, co-financed by the ESF, and from the DIPC.

A minimal model based on density-functional theory is proposed and solved to explain the unusual chemisorption properties of carbon-monooxide (CO) molecules on Cu(110)-(2 × 1)-O quasi-one-dimensional (1D) surface reported in Feng. The striking features of CO adsorption include (1) the strong lifting of the host Cu atom by 1 Å, and (2) the highly anisotropic CO-CO interaction leading to self-assembly into a nanograting structure. Our model implies that the 1D nature of the surface band is the key to these two features. We illustrate how formation of a chemical bond through specific orbital interactions between an adsorbate and 1D dispersive states of the substrate can impact the surface geometrical and electronic structure. © 2012 American Physical Society., We thank DOE-BES Division of Chemical Sciences, Geosciences, and Biosciences for support through Grant No. DE-FG02-09ER16056, W. M. Keck foundation, Ministerio de Ciencia e Innovación (Grant No. FIS2010-19609-C02-00) and G.V.-UPV/EHU (Grant No. IT-366-07) for financial support.

The interpretation of scanning tunneling spectroscopy (STS) and scanning tunneling microscopy measurements of epitaxial graphene on lattice-mismatched substrates is a challenging problem, because of the spatial modulation in the electronic structure imposed by the formation of a moiré pattern. Here we describe the electronic structure of graphene adsorbed on Ru(0001) by means of density functional theory calculations that include van der Waals interactions and are performed on a large 11×11 unit cell to account for the observed moiré patterns. Our results show the existence of localized electronic states in the high and low areas of the moiré at energies close to and well above the Fermi level, respectively. Localization is due to the spatial modulation of the graphene-Ru(0001) interaction and is at the origin of the various peaks observed in STS spectra. © 2012 American Physical Society., Work supported by the MICINN Projects No. FIS2010-15127, No. FIS2010-18847, No. CTQ2010- 17006, No. FIS-2010-19609-C09-00, No. ACI2008-0777, No. 2010C-07-25200, and No. CSD2007-00010, the CAM program NANOBIOMAGNET S2009/MAT1726, and the Gobierno Vasco-UPV/EHU Project No. IT-366-07. S.B. acknowledges financial support from MEC under FPU Grant No. AP-2007-00157.

Using first-principles calculations, the dependence in the properties of the monovacancy of graphene under rippling controlled by an isotropic strain was determined, with a particular focus on spin moments. At zero strain, the vacancy shows a spin moment of 1.5 μ B that increases to ∼2 μ B when the graphene is in tension. The changes are more dramatic under compression in that the vacancy becomes nonmagnetic when graphene is compressed more than 2%. This transition is linked to the structural changes that occur around vacancies and is associated with formation of ripples. For compressions slightly greater than 3%, this rippling leads to formation of a heavily reconstructed vacancy structure consisting of two deformed hexagons and pentagons. Our results suggest that any magnetism induced by vacancies that occurs in graphene can be controlled by applying strain. © 2012 American Chemical Society., We acknowledge the support of the Basque Departamento de Educación and the UPV/EHU (Grant No. IT-366-07), the Spanish Ministerio de Innovación, Ciencia y Tecnología (Grant No. FIS2007-66711-C02-02), and the ETORTEK research program funded by the Basque Departamento de Industria and the Diputación Foral de Guipuzcoa. EJGS acknowledges support from the CSIC JAE-predoc program, co-financed by the ESF, and from DIPC.

We investigate the chemisorption structure of CO molecules on the quasi-one-dimensional Cu(110)-(2 × 1)-O surface by low-temperature scanning tunneling microscopy and density functional theory. Contrary to flat metal surfaces, where CO molecules adsorb in an upright geometry and interact through repulsive intermolecular interactions, we find the most stable adsorption structure of single CO molecules to be at Cu atoms of substrate Cu-O- chains with the Cu-CO unit bent by ∼±45° in two equivalent structures at low coverages. At higher coverages, CO molecules combine in the same structure into highly ordered single-molecule-wide rows perpendicular to the substrate chains in an approximately 8 × 1 full monolayer structure. First-principles calculations attribute the unprecedented chemisorption behavior of CO molecules to lifting of the host Cu atoms by 1 Å from the surface Cu-O- chains, in order to optimize the bonding and reduce the repulsive interactions with the substrate. This structural distortion enables short-range intermolecular dipole-dipole attraction and creates orthogonal long-range surface-mediated repulsion leading to unusual self-assembly of CO molecules into coherent nanometer scale molecular grating structures. © 2011 American Chemical Society.

15 páginas, 6 figuras, 5 tablas., We describe an implementation of Hedin's GW approximation for molecules and clusters, the complexity of which scales as O(N3) with the number of atoms. Our method is guided by two strategies: (i) to respect the locality of the underlying electronic interactions and (ii) to avoid the singularities of Green's functions by manipulating, instead, their spectral functions using fast Fourier transform methods. To take into account the locality of the electronic interactions, we use a local basis of atomic orbitals and, also, a local basis in the space of their products. We further compress the screened Coulomb interaction into a space of lower dimensions for speed and to reduce memory requirements. The improved scaling of our method with respect to most of the published methodologies should facilitate GW calculations for large systems. Our implementation is intended as a step forward towards the goal of predicting, prior to their synthesis, the ionization energies and electron affinities of the large molecules that serve as constituents of organic semiconductors., D.S.P. and P.K. acknowledge financial support from the Consejo Superior de Investigaciones Científicas (CSIC), the Basque Departamento de Educación, UPV/EHU (Grant No. IT-366-07), the Spanish Ministerio de Ciencia e Innovación (Grant No. FIS2010-19609-C02-02), and the ETORTEK program funded by the Basque Departamento de Industria and the Diputación Foral de Guipuzcoa.

Recent developments in and around the SIESTA method of first-principles simulation of condensed matter are described and reviewed, with emphasis on (i) the applicability of the method for large and varied systems, (ii) efficient basis sets for the standards of accuracy of density-functional methods, (iii) new implementations, and (iv) extensions beyond ground-state calculations.

4 páginas, 3 figuras.-- PACS numbers: 73.22.Pr, 68.37.Ef, 68.55.-a, 71.15.Mb.-- et al., Elaborate density functional theory (DFT) calculations that include the effect of van der Waals (vdW) interactions have been carried out for graphene epitaxially grown on Ru(0001). The calculations predict a reduction of structural corrugation in the observed moiré pattern of about 25% (∼0.4 Å) with respect to DFT calculations without vdW corrections. The simulated STM topographies are close to the experimental ones in a wide range of bias voltage around the Fermi level., Work supported by the MICINN projects FIS2010-15127, FIS2010-18847, CTQ2010-17006, FIS2010-19609-C02-00, ACI2008-0777, 2010C-07- 25200, and CSD2007-00010, the CAM program NANOBIOMAGNET S2009/MAT1726, and the Gobierno Vasco—UPV/EHU project IT-366-07.

6 páginas, 5 figuras., Femtosecond and subfemtosecond time scales typically rule electron dynamics at metal surfaces. Recent advance in experimental techniques permits now remarkable precision in the description of these processes. In particular, shorter time scales, smaller system sizes, and spin-dependent effects are current targets of interest. In this article, we use state-of-the-art theoretical methods to analyze these refined features of electron dynamics. We show that the screening of localized charges at metal surfaces is created locally in the attosecond time scale, while collective excitations transfer the perturbation to larger distances in longer time scales. We predict that the elastic width of the resonance in excited alkali adsorbates on ferromagnetic surfaces can depend on spin orientation in a counterintuitive way. Finally, we quantitatively evaluate the electron–electron and electron–phonon contributions to the electronic excited states widths in ultrathin metal layers. We conclude that confinement and spin effects are key factors in the behavior of electron dynamics at metal surfaces., We acknowledge partial support by the Basque government, the University of the Basque Country UPV/EHU (Grant No. 9/UPV 00206.215-13639/2001), and the Spanish Ministerio de Educación y Ciencia (Grant FIS2007-66711-C02-00).

5 páginas, 4 figuras., The transport of charge through a conducting material depends on the intrinsic ability of the material to conduct current and on the charge injection efficiency at the contacts between the conductor and the electrodes carrying current to and from the material1, 2, 3. According to theoretical considerations4, this concept remains valid down to the limit of single-molecule junctions5. Exploring this limit in experiments requires atomic-scale control of the junction geometry. Here we present a method for probing the current through a single C60 molecule while changing, one by one, the number of atoms in the electrode that are in contact with the molecule. We show quantitatively that the contact geometry has a strong influence on the conductance. We also find a crossover from a regime in which the conductance is limited by charge injection at the contact to a regime in which the conductance is limited by scattering at the molecule. Thus, the concepts of ‘good’ and ‘bad’ contacts, commonly used in macro- and mesoscopic physics, can also be applied at the molecular scale., This work was supported by the Deutsche Forschungsgemeinschaft (SFB 677), the Schleswig–Holstein Fonds, the Ministerio de Cienciae Innovacion (FIS2007-6671) and the Basque Department of Education (IT-366-07).

Low-temperature scanning tunneling microscopy and density-functional theory (DFT) were used to study the adsorption of water on a Ru(0001) surface covered with half monolayer of oxygen. The oxygen atoms occupy hcp sites in an ordered structure with $(2\ifmmode\times\else\texttimes\fi{}1)$ periodicity. DFT predicts that water is weakly bound to the unmodified surface, 86 meV compared to the $\ensuremath{\sim}200\text{ }\text{meV}$ water-water H bond. Instead, we found that water adsorption causes a shift of half of the oxygen atoms from hcp sites to fcc sites, creating a honeycomb structure where water molecules bind strongly to the exposed Ru atoms. The energy cost of reconstructing the oxygen overlayer, around 230 meV per displaced oxygen atom, is more than compensated by the larger adsorption energy of water on the newly exposed Ru atoms. Water forms hydrogen bonds with the fcc O atoms in a $(4\ifmmode\times\else\texttimes\fi{}2)$ superstructure due to alternating orientations of the molecules. Heating to 185 K results in the complete desorption of the water layer, leaving behind the oxygen-honeycomb structure, which is metastable relative to the original $(2\ifmmode\times\else\texttimes\fi{}1)$. This stable structure is not recovered until after heating to temperatures close to 260 K.

4 páginas, 3 figuras, 1 tabla.-- PACS numbers: 68.37.Ef, 72.10.-d, 72.25.-b, 79.20.Rf, Density functional theory simulations of the vibrational inelastic electron tunneling spectroscopy (IETS) of O2 on Ag(110) permits us to solve its unexplained IETS data [ Hahn et al. Phys. Rev. Lett. 85 1914 (2000)]. When semilocal density functional theory is corrected by including static intra-atomic correlations, the IETS simulations are in excellent agreement with the experiment. The unforeseen consequence of our calculations is that when adsorbed along the [001] direction, molecular O2 on Ag(110) is a mixed-valent system. This analysis of IETS unambiguously reveals the paramagnetic nature of O2 on Ag(110)., We acknowledge financial support from the Spanish MICINN (No. FIS2007-066711-CO2-00 and No. FIS2009-12721-C04-01), and the Basque Government—UPV/EHU (Grant No. IT-366-07).

7 páginas, 5 figuras., We have performed a density functional theory study of the possible layered geometries occurring after dehydrogenation of a self-assembled monolayer (SAM) of biphenyl-thiol molecules (BPTs) adsorbed on Au(111), as it has been experimentally observed for low energy electron irradiated SAMs of 4′-nitro-1,1′-biphenyl-thiol adsorbed on a Au(111) surface. [Eck et al., Advanced Materials 2000, 12, 805] Cross-link formation between the BPT molecules has been analyzed using different models with different degrees of complexity. We start by analyzing the bonding between biphenyl (BP) molecules in a lineal dimer and their characteristic vibration frequencies. Next, we consider the most stable cross-linked structures formed in an extended free-standing monolayer of fully dehydrogenated BP molecules. Finally, we analyze a more realistic model where the role of the Au(111) substrate and sulfur head groups is explicitly taken into account. In this more complex model, the dehydrogenated BPT molecules are found to interact covalently to spontaneously form “graphene-like” nanoflakes. We propose that these nanographenes provide plausible building-blocks for the structure of the carbon layers formed by electron irradiation of BPT-SAMs. In particular, it is quite tempting to visualize those structures as the result of the cross-link and entanglement of such graphene nanoflakes., We acknowledge support from Basque Departamento de Educación, UPV/EHU (grant no. IT-366-07), the Spanish Ministerio de Educación y Ciencia (grant no. FIS2007- 66711-C02-00) and the ETORTEK research program funded by the Basque Departamento de Industria and the Diputación Foral de Guipúzcoa.

5 páginas, 4 figuras.-- PACS number(s): 73.40.-c, 31.10.+z, 63.22.-m, 73.63.Rt.-- et al., We study pentanedithiol molecular junctions formed by means of the break-junction technique with a scanning tunneling microscope at low temperatures. Using inelastic electron tunneling spectroscopy and first-principles calculations, the response of the junction to elastic deformation is examined. We show that this procedure makes a detailed characterization of the molecular junction possible. In particular, our results indicate that tunneling takes place through just a single molecule., This work has been supported by the Spanish MICINN (Grants No. MAT2008-01735, No. FIS2007-6671-C02-00, and No. MAT2007-62732, and Consolider-Ingenio 2010 under Grant No. CSD2007-0010), the CAM (“CITECNOMIK” Grant No. P-ESP-000337- 0505), the UPV/EHU (Grant No. IT-366-07), and the Basque Depto. de Industria and the Diputación Foral de Guipuzcoa (“ETORTEK”), the EC (STREP “SURFMOF” Grant No. NMP4-CT-2006-032109, and FP7 ITN “FUNMOLS” Grant No. 212942). T.F. acknowledges support from the Danish FNU (Grant No. 272-07-0114).

6 páginas, 4 figuras.-- PACS number(s): 73.90.+f, 75.70.-i, 61.48.De, We report ab initio calculations of the structural, electronic, and magnetic properties of a graphene monolayer substitutionally doped with Co (Cosub) atoms. These calculations are done within density-functional theory using the generalized gradient approximation. We focus in Co because among traditional ferromagnetic elements (Fe, Co, and Ni), only Cosub atoms induce spin polarization in graphene. Our results show the complex magnetism of Co substitutional impurities in graphene, which is mapped into simple models such as the π-vacancy and Heisenberg model. The links established in our work can be used to bring into contact the engineering of nanostructures with the results of π models in defective graphene. In principle, the structures considered here can be fabricated using electron irradiation to create defects and depositing Co at the same time., We acknowledge support from Basque Dep. de Educación and the UPV/EHU (Grant No. IT-366-07) and the Spanish MCI (Grant No. FIS2007-66711-C02-02).

3 páginas, 3 figuras.-- et al., Infrared spectroscopy is demonstrated to sensitively detect electronic excitations in 1-nm-wide wires made of indium. The polarization-dependent spectra measured at room temperature show a strong broadband plasmonic absorption feature in the direction parallel to the wires, while in the perpendicular direction the wires stay nearly transparent in the same spectral range. At 88 K the wires do not show this broadband absorption anymore, but instead, several interband-transition features arise for both polarizations, in agreement to the gap opening of the metal-to-insulator transition as known for this one-dimensional structure., This work is a part of the joint project “Strategic International Cooperative Program” funded by DFG-Germany (Grant No. PU193/9) and JST-Japan, and Spanish MICINN (Grant No. FIS2007-66711-C02-02) and Grant-in-Aid for Scientific Research from the Ministry of Education, Culture, Sports, Science, and Technology (MEXT).

4 páginas, 4 figuras.-- PACS numbers: 73.20.-r, 68.37.Ef, 68.55.-a, 73.22.Pr.-- et al., We explore the spatial variations of the unoccupied electronic states of graphene epitaxially grown on Ru(0001) and observed three unexpected features: the first graphene image state is split in energy; unlike all other image states, the split state does not follow the local work function modulation, and a new interfacial state at þ3 eV appears on some areas of the surface. First-principles calculations explain the observations and permit us to conclude that the system behaves as a self-organized periodic array of quantum dots., Financial support by the Spanish MICINN through project CONSOLIDER-INGENIO 2010 on Molecular Nanoscience and Grants No. FIS2007-61114 and No. FIS2007-6671, Comunidad de Madrid through the program NANOBIOMAGNET S-2009/MAT1726, the Basque Government (Grant No. IT-366-07 and inanoGUNE projects) is gratefully acknowledged., S-2009/MAT-1726/Nanobiomagnet

9 páginas, 6 figuras, 2 tablas.-- PACS number(S): 33.15.Fm, 68.43.-h, 33.15.Kr, Density functional theory calculations are used to investigate the role of substrate-induced cooperative effects on the adsorption of water on a partially oxidized transition-metal surface, O(2×2)/Ru(0001). Focusing particularly on the dimer configuration, we analyze the different contributions to its binding energy. A significant reinforcement of the intermolecular hydrogen bond (H bond), also supported by the observed frequency shifts of the vibration modes, is attributed to the polarization of the donor molecule when bonded to the Ru atoms in the substrate. This result is further confirmed by our calculations for a water dimer interacting with a small Ru cluster, which clearly show that the observed effect does not depend critically on fine structural details and/or the presence of coadsorbates. Interestingly, the cooperative reinforcement of the H bond is suppressed when the acceptor molecule, instead of the donor, is bonded to the surface. This simple observation can be used to rationalize the relative stability of different condensed structures of water on metallic substrates., We acknowledge support from Basque Departamento de Educación, UPV/EHU (Grant No. IT-366-07), the Spanish Ministerio Innovación y Ciencia (Grant No. FIS2007-66711- C02-00), and the ETORTEK research program funded by the Basque Departamento de Industria and the Diputación Foral de Guipúzcoa. M.V.F.-S. acknowledges support from DOE under Grant No. DE-FG02-09ER16052.

4 páginas, 3 figuras., Molecular junctions have been characterized to determine the influence of the metal contact formation in the electron transport process through a single molecule. With inelastic electron tunneling spectroscopy and first-principles calculations, the vibration modes of a carbon monoxide molecule have been surveyed as a function of the distance from a copper electrode with unprecedented accuracy. We observe a continuous but nonlinear blue shift of the frustrated rotation mode in tunneling with decreasing distance followed by an abrupt softening upon contact formation. This indicates that the presence of the metal electrode sensibly alters the structural and conductive properties of the junction even without the formation of a strong chemical bond., Support from the Basque Departamento de Educación, UPV/EHU (Grant No. IT-366-07), the Spanish Ministerio de Ciencia e Innovación (Grants No. FIS2007-6671-C02-00, and MAT2007-62732), the ETORTEK program funded by the Basque Departamento de Industria and the Diputacion Foral de Guipuzcoa, and the Danish FNU (Grant No. 272-07-0114) are gratefully acknowledged.

32 páginas, 13 figuras, 3 tablas., We present a theoretical study using density functional calculations of the structural, electronic and magnetic properties of 3d transition metal, noble metal and Zn atoms interacting with carbon monovacancies in graphene. We pay special attention to the electronic and magnetic properties of these substitutional impurities and find that they can be fully understood using a simple model based on the hybridization between the states of the metal atom, particularly the d shell, and the defect levels associated with an unreconstructed D3h carbon vacancy. We identify three different regimes associated with the occupation of different carbon–metal hybridized electronic levels: (i) bonding states are completely filled for Sc and Ti, and these impurities are non-magnetic; (ii) the non-bonding d shell is partially occupied for V, Cr and Mn and, correspondingly, these impurities present large and localized spin moments; (iii) antibonding states with increasing carbon character are progressively filled for Co, Ni, the noble metals and Zn. The spin moments of these impurities oscillate between 0 and 1μB and are increasingly delocalized. The substitutional Zn suffers a Jahn–Teller-like distortion from the C3v symmetry and, as a consequence, has a zero spin moment. Fe occupies a distinct position at the border between regimes (ii) and (iii) and shows a more complex behavior: while it is non-magnetic at the level of generalized gradient approximation (GGA) calculations, its spin moment can be switched on using GGA+U calculations with moderate values of the U parameter., We acknowledge support from Basque Departamento de Educación and the UPV/EHU (grant no IT-366-07), the Spanish Ministerio de Educación y Ciencia (grant no FIS2007-66711- C02-02) and the ETORTEK program funded by the Basque Departamento de Industria and the Diputación Foral de Guipuzcoa.

We report ab initio calculations of zirconium-coated graphene sheets at several coverages and geometries. We calculate adsorption properties, such as distances and the Zr/graphene binding energies. When increasing the Zr/C coverage ratio, the binding energies show that the Zr atoms have a trend to cluster. The most stable Zr/C coverage corresponds to 0.375, which has no stress between the zirconium and graphene layer. The Zr-graphene binding involves charge transfer to graphene which comes from the $5s$ orbital of Zr and depends on the coverage. We also calculate the diffusion-energy barriers on graphene for the single atom and the ${\text{Zr}}_{3}$ trimer and we see that the ${\text{Zr}}_{3}$ cluster is a faster diffusion unit. We also estimate that the Zr diffusion energy between two substitutional positions is at least 4 eV, which is large enough to fix Zr atoms bound to C vacancies at actual temperatures in high-resolution transmission electronic microscopy experiments.

Using time-dependent density functional theory we calculate from first-principles the rate of energy transfer from a moving charged particle to the electrons in an insulating material. The behavior of the electronic stopping power in LiF (a wide band gap insulator) versus projectile velocity displays an effective threshold velocity of 8.2 Bohr/asec for the proton, consistent with recent experimental observations. The calculated proton/antiproton stopping power ratio is 2.4 at velocities slightly above the threshold (16.5 Bohr/asec) as compared to the experimental value of 2.1. The approximations introduced in this new non-perturbative methodology are discussed, and results on the velocity dependence of the stopping power, the locality of the energy transfer, and other characteristics of the host material are presented., This work has been funded by the EC’s Marie Curie program, UK’s BNFL and NERC, the Spanish MEC, the UPV/EHU and the Basque Government through the Etortek program.

Magnetic properties of graphenic carbon nanostructures, which are relevant for future spintronic applications, depend crucially on doping and on the presence of defects. In this paper we study the magnetism of the recently detected substitutional Ni (Nisub) impurities. Nisub defects are nonmagnetic in flat graphene and develop a nonzero-spin moment only in metallic nanotubes. This surprising behavior stems from the peculiar curvature dependence of the electronic structure of Nisub. A similar magnetic-nonmagnetic transition of Nisub can be expected by applying anisotropic strain to a flat graphene layer., E.J.G.S., A.A., and D.S.P. acknowledge support from the Basque Government and UPV/EHU Grant No. IT-366-07, CSIC, the Spanish MEC Grant No. FIS2007-66711-C02-02, and the Basque Government and Diputación Foral de Guipuzcoa through the ETORTEK program. A.G.S.F. acknowledges the support from Brazilian agencies FUNCAP, CAPES/FAPERGS, CNPq Grant No. 306335/2007-7, Rede Nacional de Pesquisa em Nanotubos de Carbono, Rede de Nanobioestruturas, and Instituto do Milenio de Nanotecnologia CNPq/MCT-Brazil.

Chemisorption of atoms and molecules controls many interfacial phenomena such as charge transport and catalysis. The question of how the intrinsic properties of the interacting materials define the electronic structure of their interface remains one of the most important, yet intractable problems in surface physics. Through two-photon photoemission spectroscopy we determine a common binding energy of $\ensuremath{\sim}1.8--2.0\text{ }\text{eV}$ with respect to the vacuum for the unoccupied resonance of the $ns$ valence electron of alkali atoms (Li-Cs) chemisorbed at low coverage (less than 0.1 monolayer) on noble metal [Cu(111) and Ag(111)] surfaces. We present a theoretical model based on the semiempirical potentials of the adsorbates and the substrates, their principal mode of interaction through the Coulomb interaction, and the ab initio adsorption structures. Our analysis reveals that atomic size and ionization potential independent interfacial electronic structure is a consequence of the Coulomb interaction among the $ns$ electron, the alkali-atom ionic core, and the induced image charge in the substrate. We expect the same interactions to define the effective electronic potentials for a broad range of molecule/metal interfaces.

Using density-functional theory we found that, depending on coverage, coadsorbed oxygen can act both as a promoter and as an inhibitor of the dissociation of water on Ru(0001), the transition between these two behaviors occurring at ∼0.2 ML. The key factor that determines this transition is the adsorption energy of the reaction products, OH in particular. The chemistry of this coadsorbed system is dictated by the effective coordination of the Ru atoms that participate in the bonding of the different species. In particular, we observed that a low coverage of oxygen increases the adsorption energy of the OH fraction on the Ru surface. This surprising extra stabilization of the OH with the coadsorption of oxygen can be understood in the context of the metallic bonding and could well correspond to a general trend for the coadsorption of electronegative species on metallic surfaces., We acknowledge support from the Basque Departamento de Educación, UPV/EHU Grant No. IT-366-07, the Spanish Ministerio de Educación y Ciencia Grant No. FIS2007-66711-C02-02, and ETORTEK research contracts funded by the Basque Departamento de Industria and the Diputación Foral de Guipuzcoa. The work at the Berkeley Lab was supported by the Director, Office of Science, Office of Basic Energy Sciences, Materials Sciences and Engineering Division, of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. The work of A.M. was financed by the Marie Curie Outgoing International Fellowship, Project No. 514412.

We present an ab initio scheme for the calculation of the resonant charge transfer of electrons at surfaces. The electron initially resides in a bound resonance, i.e., appearing below the vacuum level, associated with a core-excited adsorbate. Our treatment is based on first-principles density-functional calculations of this initial situation using finite slabs. These results are combined with bulk calculations of the substrate material to obtain the Hamiltonian of the semi-infinite system in which the electron evolves. Therefore, we include a realistic description of the electronic structure of both subsystems, substrate and adsorbate, and the interaction between them. The surface Green's function is then computed using the transfer matrix method and projected onto a wave packet localized in the adsorbate. The width and energy of the resonance can be obtained from an analysis of the projected Green's function, and the charge transfer time can be estimated. The calculated width is independent of the wave packet used for the projection, at least as far as there are not several overlapping resonances at neighboring energies. Alternatively, one can directly calculate the time evolution of the population of the initial wave packet. Both alternatives are presented and compared. Our first-principles calculations are based on periodic arrangements of adsorbates on the surface. With an appropriate average of the ${\mathbf{k}}_{\ensuremath{\parallel}}$ resolved results, one can extrapolate to the limit of an isolated adsorbate. We discuss several possibilities to do this. As an application, we focus on the case of the $4s$ bound resonance of a core-excited ${\mathrm{Ar}}^{*}(2{p}_{3∕2}^{\ensuremath{-}1}4s)$ adsorbate on Ru(0001), for which there are extensive experimental studies. The calculated values and trends are in good agreement with the experimental observations.

We present a combined theoretical and experimental study of water adsorption on Ru(0001) pre-covered with 0.25 monolayers (ML) of oxygen forming a (2 x 2) structure. Several structures were analyzed by means of Density Functional Theory calculations for which STM simulations were performed and compared with experimental data. Up to 0.25 monolayers the molecules bind to the exposed Ru atoms of the 2 x 2 unit cell via the lone pair orbitals. The molecular plane is almost parallel to the surface with its H atoms pointing towards the chemisorbed O atoms of the 2 x 2 unit cell forming hydrogen bonds. The existence of these additional hydrogen bonds increases the adsorption energy of the water molecule to approximately 616 meV, which is {approx}220 meV more stable than on the clean Ru(0001) surface with a similar configuration. The binding energy shows only a weak dependence on water coverage, with a shallow minimum for a row structure at 0.125 ML. This is consistent with the STM experiments that show a tendency of the molecules to form linear rows at intermediate coverage. Our calculations also suggest the possible formation of water dimers near 0.25 ML.

The quasi-one-dimensional Si(557)-Au reconstruction has attracted a lot of attention in recent years. We study here the interplay between the electronic and structural degrees of freedom in this system. Our calculations are in good agreement with recent experimental data obtained using scanning tunneling microscopy and spectroscopy both at room and low temperatures. Together with the quite successful description of the experimental band structure, these results give further support to the current structural model of the Si(557)-Au surface. We consider in detail the energetics and variation of the band structure as a function of the buckling of the step edge and its implications to explain the observed metal-insulator transition. Finally, we present the results of a first-principles molecular dynamics simulation of several picoseconds performed at room temperature. As expected, we find a strong oscillation of the step-edge atoms. The dynamics associated with other vibrational modes is also observed. Particularly apparent are the oscillations of the height of the restatoms and adatoms and the associated fluctuation of the Si–Au–Si bond angles along the gold chain. This mode, together with step-edge buckling, has a strong influence on the insulating and/or metallic character of the surface., This work was supported by the Basque Departamento de Educación and the UPV/EHU Grant No. 9/UPV 00206.215-13639/2001, the Spanish Ministerio de Educacón y Ciencia Grant No. FIS2004-06490-C3-02, the European Network of Excellence FP6-NoE “NANOQUANTA” Grant No. 500198-2, and the research contracts “Nanomateriales” and “Nanotron” funded by the Basque Departamento de Industria, Comercio y Turismo within the ETORTEK program and the Departamento para la Innovación y la Sociedad del Conocimiento from the Diputación Foral de Guipuzcoa.

We present an atomic-orbital-based approximate scheme for self-interaction correction (SIC) to the local-density approximation (LDA) of density-functional theory. The method, based on the idea of Filippetti and Spaldin [Phys. Rev. B 67, 125109 (2003)], is implemented in a code using localized numerical atomic-orbital basis sets and is now suitable for both molecules and extended solids. After deriving the fundamental equations as a nonvariational approximation of the self-consistent SIC theory, we present results for a wide range of molecules and insulators. In particular, we investigate the effect of re-scaling the self-interaction correction and we establish a link with the existing atomiclike corrective scheme LDA+U. We find that when no re-scaling is applied, i.e., when we consider the entire atomic correction, the Kohn-Sham highest occupied molecular orbital (HOMO) eigenvalue is a rather good approximation to the experimental ionization potential for molecules. Similarly the HOMO eigenvalues of negatively charged molecules reproduce closely the molecular affinities. In contrast a re-scaling of about 50% is necessary to reproduce insulator band gaps in solids, which otherwise are largely overestimated. The method therefore represents a Kohn-Sham based single-particle theory and offers good prospects for applications where the actual position of the Kohn-Sham eigenvalues is important, such as quantum transport., This work was supported by the Science Foundation of Ireland under Grant No. SFI02/IN1/I175. D.S.P. acknowledges financial support from the University of the Basque Country Grant No. 9/UPV 00206.215-13639/2001, the Spanish Ministerio de Educacion y Ciencia Grant No. FIS2004-06490-C03-00, and the Basque Goverment and Diputacion Foral de Giupuzkoa NANOMATERIALES and NANOTRON grants, ETORTEK program.

We present here a comprehensive search for the structure of the Si(553)-Au reconstruction. More than two hundred different trial structures have been studied using first-principles density-functional calculations with the SIESTA code. An iterative procedure, with a step-by-step increase of the accuracy and computational cost of the calculations, was used to allow for the study of this large number of configurations. We have considered reconstructions restricted to the topmost bilayer and studied two types: i) "flat" surface-bilayer models, where atoms at the topmost bilayer present different coordinations and registries with the underlying bulk, and ii) nine different models based on the substitution of a silicon atom by a gold atom in different positions of a $\pi$-bonded chain reconstruction of the Si(553) surface. We have developed a compact notation that allows us to label and identify all these structures. This is very useful for the automatic generation of trial geometries and counting the number of inequivalent structures, i.e., structures having different bonding topologies. The most stable models are those that exhibit a honeycomb-chain structure at the step edge. One of our models (model f2) reproduces the main features of the room temperature photoemission and scanning-tunneling microscopy data. Thus we conclude that f2 structure is a good candidate for the high temperature structure of the Si(553)-Au surface., Comment: Submitted to Phys. Rev. B on December 10, 2007

Using time-dependent density-functional theory we calculate from first principles the rate of energy transfer from a moving proton or antiproton to the electrons of an insulating material, LiF. The behavior of the electronic stopping power versus projectile velocity displays an effective threshold velocity of ∼0.2a.u. for the proton, consistent with recent experimental observations, and also for the antiproton. The calculated proton/antiproton stopping-power ratio is ∼2.4 at velocities slightly above the threshold (v∼0.4a.u.), as compared to the experimental value of 2.1. The projectile energy loss mechanism is observed to be extremely local., This work has been funded by the EC’s Marie Curie program, UK’s BNFL and NERC, the Spanish MEC, the UPV/EHU and the Basque Government through the Etortek program.

Recent advances in the theoretical description of dynamic screening and electron dynamics in metallic media are reviewed. The time-dependent building-up of screening in different situations is addressed. Perturbative and non-perturbative theories are used to study electron dynamics in low-dimensional systems, such as metal clusters, image states, surface states and quantum wells. Modification of the electronic lifetimes due to confinement effects is analyzed as well. © 2006 Elsevier B.V. All rights reserved., We acknowledge partial support by the University of the Basque Country UPV/EHU (Grant No. 9/UPV 00206.215-13639/2001), and the Spanish MCyT (Grant No. FIS2004-06490-CO3-00).

The decay rates of electron and hole excitations at metal surfaces as determined by a scanning tunnelling microscope are presented and discussed. Surface-localised electron states as diverse as Shockley-type surface states and quantum well states confined to ultrathin alkali metal adsorption layers are covered. Recent developments in the analysis of the experimental procedures that are used to determine decay rates with the scanning tunnelling microscope, namely the analysis of line shapes and the spatial decay of standing wave patterns, are discussed., Financial support by the Deutsche Forschungsgemeinschaft and the British Council is gratefully acknowledged. This work has been supported by the Basque Departamento de Educación, the UPV/EHU, the Spanish Ministerio de Educación y Ciencia, the European Network of Excellence FP6-NoE NANOQUANTA, and the projects NANOMATERIALES and NANOTRON funded by the Basque Departamento de Industria, Comercio y Turismo within the ETORTEK programme and the Departamento para la Innovación y la Sociedad del Conocimiento from the Diputación Foral de Guipúzcoa.

The authors have investigated the structure and energetics of the first hydration layer on NaCl(100) by means of density functional calculations. They have analyzed in detail the role of the hydrogen bond between the adsorbed molecules for the determination of the most favorable structures. They have shown that, using the water dimers as basic building blocks, very stable structures can be constructed. They discuss here two important examples: (i) a model with (1×1) periodicity at 2 ML coverage, and (ii) icelike bilayers with a c(4×2)unit cell at 1.5 ML. Both structures present high adsorption energies per water molecule of ∼570meV, in comparison to the 350meV adsorption energy obtained for the previously studied (1×1) structures composed of weakly interacting monomers. Based on these findings, they propose an interpretation for the experimental observations of Toennies et al. [J. Chem. Phys. 120, 11347 (2004)], who found a transition of the periodicity of the first hydration layer on NaCl(100) from (1×1) to c(4×2) upon electron irradiation. According to the model, the transition would be driven by the partial desorption of (1×1) bilayer structures corresponding to a local coverage of 2 ML and the further rearrangement of the remaining water molecules to form a quasihexagonal structure with c(4×2) periodicity at coverage close to 1.5 ML., This work has been supported by the Basque Departamento de Educación, the UPV/EHU (Grant No. 9/UPV 00206.215-13639/2001), the Spanish Ministerio de Educación y Ciencia (Grant No. FIS2004-06490-C3-00), the European Network of Excellence FP6-NoE “NANOQUANTA” (Grant No. 500198-2), and the projects “NANOMATERIALES” and “NANOTRON” funded by the Basque Departamento de Industria, Comercio y Turismo within the ETORTEK programme and the Departamento para la Innovación y la Sociedad del Conocimiento from the Diputación Foral de Guipúzcoa.

Cement-based materials are ubiquitous in almost all built environment. In spite of this, little is known about the formation and the role played by the silicate chains always present in the cement nanostructure. By means of first principles simulations we provide compelling evidence on the pivotal role played by certain ionic species in the formation of the silicate chains inside the cementitious matrix. Moreover, we corroborate the experimental evidence which shows that the length of the most stable chains with m Si atoms follows a magic-number sequence: m=3n-1 with n=1,2,... Our results have been applied in the development of new higher performance cement-based materials by adding nanosilica. © 2007 American Institute of Physics.

Time-dependent density-functional theory is used to calculate quantum-size effects in the energy loss of antiprotons interacting with a confined two-dimensional electron gas. The antiprotons follow a trajectory normal to jellium circular clusters of variable size, crossing every cluster at its geometrical center. Analysis of the characteristic time scales that define the process is made. For high-enough velocities, the interaction time between the projectile and the target electrons is shorter than the time needed for the density excitation to travel along the cluster. The finite-size object then behaves as an infinite system, and no quantum-size effects appear in the energy loss. For small velocities, the discretization of levels in the cluster plays a role and the energy loss does depend on the system size. A comparison to results obtained using linear theory of screening is made, and the relative contributions of electron-hole pair and plasmon excitations to the total energy loss are analyzed. This comparison also allows us to show the importance of a nonlinear treatment of the screening in the interaction process. © 2006 The American Physical Society., This work was supported, in part, by the Basque Departamento de Educación, Universidades e Investigación, the University of the Basque Country UPV/EHU (Grant No. 9/UPV 00206.215-13639/2001), the Spanish Ministerio de Educación y Ciencia (Grant No. FIS2004-06490-C03-00), and the EU Network of Excellence NANOQUANTA (Grant No. NMP4-CT-2004-500198). A.G.B. acknowledges financial support by the DIPC.

arXiv:cond-mat/0512618v1, Using X-ray diffraction Ghose et al. [S.K. Ghose, I.K. Robinson, P.A. Bennett, F.J. Himpsel, Surf. Sci. 581 (2005) 199] have recently produced a structural model for the quantum-wire surface Si(5 5 3)–Au. This model presents two parallel gold wires located at the step edge. Thus, the structure and the gold coverage are quite different from previous proposals. We present here an ab initio study using density functional theory of the stability, electronic band structure and scanning tunneling microscopy images of this model., This work was supported by the Basque Departamento de Educación, the UPV/EHU (Grant No. 9/UPV 00206.215-13639/2001), the Spanish Ministerio de Educacón y Ciencia (Grant No. FIS2004-06490-C3-02), and the European Network of Excellence FP6-NoE “NANOQUANTA” (500198-2). SR also acknowledges support from the Magnus Ehrnroot Foundation.

We gratefully acknowledge support by the Department of Education of the Government of the Basque Country, Spanish MCyT (Grant No. MAT2001-0946), and the European Community 6th Network of Excellence NANOQUANTA (NMP4-CT-2004-500198).

The metal–insulator transition observed in the In/Si(1 1 1)-4 × 1 reconstruction is studied by means of ab initio calculations of a simplified model of the surface. Different surface bands are identified and classified according to their origin and their response to several structural distortions. We support the, recently proposed [C. González, J. Ortega, F. Flores, New J. Phys. 7 (2005) 100], combination of a shear and a Peierls distortions as the origin of the metal–insulator transition. Our results also seem to favor an electronic driving force for the transition., This work was supported by the Basque Departamento de Educación and the UPV/EHU, the Basque Departamento de Industria (project NANOMAT, ETORTEK program), the Spanish MEC, and the European Network of Excellence FP6-NoE “NANOQUANTA”. S.R. also acknowledges support from the Magnus Ehrnroot foundation.

We present a systematic study of the atomic and electronic structure of the $\mathrm{Si}(111)\text{\ensuremath{-}}(5\ifmmode\times\else\texttimes\fi{}2)\text{\ensuremath{-}}\mathrm{Au}$ reconstruction using first-principles electronic structure calculations based on the density functional theory. We analyze the structural models proposed by Marks and Plass [Phys. Rev. Lett. 75, 2172 (1995)], those proposed recently by Erwin [ Phys. Rev. Lett. 91, 206101 (2003)], and a completely different structure that was found during our structural optimizations. We study in detail the energetics and the structural and electronic properties of the different models. For the two most stable models, we also calculate the change in the surface energy as a function of the content of silicon adatoms for a realistic range of concentrations. Our model is the energetically most favorable in the range of low adatom concentrations, while Erwin's ``$5\ifmmode\times\else\texttimes\fi{}2$'' model becomes favorable for larger adatom concentrations. The crossing between the surface energies of both structures is found close to $1∕2\phantom{\rule{0.3em}{0ex}}\text{adatom}\phantom{\rule{0.3em}{0ex}}\text{per}\phantom{\rule{0.3em}{0ex}}5\ifmmode\times\else\texttimes\fi{}2\phantom{\rule{0.3em}{0ex}}\text{unit}\phantom{\rule{0.3em}{0ex}}\text{cell}$, i.e., near the maximum adatom coverage observed in the experiments. Both models, our structure and Erwin's ``$5\ifmmode\times\else\texttimes\fi{}2$'' model, seem to provide a good description of many of the available experimental data, particularly of the angle-resolved photoemission measurements.

Recent photoemission experiments on the Si(553)-Au reconstruction show a one-dimensional band with a peculiar ~1/4 filling. This band could provide an opportunity for observing large spin-charge separation if electron-electron interactions could be increased. To this end, it is necessary to understand in detail the origin of this surface band. A first step is the determination of the structure of the reconstruction. We present here a study of several structural models using first-principles density functional calculations. Our models are based on a plausible analogy with the similar and better known Si(557)-Au surface, and compared against the sole structure proposed to date for the Si(553)-Au system [Crain JN et al., 2004 Phys. Rev. B 69 125401 ]. Results for the energetics and the band structures are given. Lines for the future investigation are also sketched.

Practical quantum mechanical simulations of materials, which take into account explicitly the electronic degrees of freedom, are presently limited to about 1000 atoms. In contrast, the largest classical simulations, using empirical interatomic potentials, involve over 109 atoms. Much of this 106-factor difference is due to the existence of well-developed order-N algorithms for the classical problem, in which the computer time and memory scale linearly with the number of atoms N of the simulated system. Furthermore, such algorithms are well suited for execution in parallel computers, using rather small interprocessor communications. In contrast, nearly all quantum mechanical simulations involve a computational effort which scales as O(N 3 ), that is, as the cube of the number of atoms simulated. Such an intrinsically more expensive dependence is due to the delocalized character of the electron wavefunctions. Since the electrons are fermions, every one of the ~N occupied wavefunctions must be kept orthogonal to every other one, thus requiring ~N 2 constraints, each involving an integral over the whole system, whose size is also proportional to N.

Scanning tunneling spectroscopy of p(2x2) Cs and Na ordered overlayers on Cu(111) reveals similar line widths of quasi two-dimensional quantum well states despite largely different binding energies. Detailed calculations show that 50% of the line widths are due to electron-phonon scattering while inelastic electron-electron scattering is negligible. A frequently ignored mechanism for ordered structures, i.e., enhanced elastic scattering due to Brillouin zone back folding, contributes the remaining width., Comment: 4 pages, 2 figures, 1 table

Using three different density functional packages. DMol 3 , VASP, and SIESTA, we have calculated the relaxed structures and relative energies of the diastereomers of cyclic phosphoric acid and its chlorine derivative with ephedrine. The structures predicted by the three codes are in very good agreement with experiment. Also in accordance with experiment, very small energy differences (

The mechanism for the ferromagnetic order of (Ga,Mn)As and (Ga,Mn)N is extensively studied over a vast range of Mn concentrations. We calculate the electronic structures of these materials using density functional theory in both the local spin density approximation (LSDA) and the local density approximation (LDA)+U scheme, that we have now implemented in the code SIESTA. For (Ga,Mn)As, the LDA+U approach leads to a hole mediated picture of the ferromagnetism, with an exchange constant Nβ=−2.8eV. This is smaller than that obtained with LSDA, which overestimates the exchange coupling between Mn ions and the As p holes. In contrast, the ferromagnetism in wurtzite (Ga,Mn)N is caused by the double-exchange mechanism, since a hole of strong d character is found at the Fermi level in both the LSDA and the LDA+U approaches. In this case the coupling between the Mn ions decays rapidly with the Mn-Mn separation. This suggests a two phases picture of the ferromagnetic order in (Ga, Mn)N, with a robust ferromagnetic phase at large Mn concentration coexisting with a diluted weak ferromagnetic phase., This work is sponsored by Enterprise Ireland under the grant EI-SC/2002/10. Traveling is sponsored by Enterprise Ireland under the International Collaboration programme EIIC/2003/47. D.S.-P. acknowledges support by the Basque Departamento de Educación, the UPV/EHU (Grant. No. 9/UPV 00206.215-13639/2001), and the Spanish MEC (Grant No. FIS2004-06490-C03-02).

A rich variety of competing phases is predicted for nitrogen at accessible pressures, including a new metallic chainlike phase very close in energy to the previously predicted cubic gauche phase, and other phases at slightly higher energies, e.g., one with N2 and N6 units. Large energy barriers between structures can account for recent observations of metastability, and we identify a low barrier transition path from the known ε phase to the chainlike metallic phase. In analogy to MgB2, the metal is anisotropic with multiple Fermi surfaces formed from π and σ states., We gratefully acknowledge funding from the Center for Simulation of Advanced Rockets at the University of Illinois Urbana-Champaign, supported by the U.S. DOE through the University of California, Subcontract No. B523819. The work was also supported by the DOD MURI Grant No. AA-5-7232-A1 managed by the Army Research Office. Computational support was provided by the Materials Computation Center and the National Center for Supercomputing Applications at the University of Illinois, and the Major Shared Research Center of the Army Research Laboratory. D. S.-P. acknowledges support from Spanish MCyT under the ‘‘Ramon y Cajal’’ program.

The use of quantum mechanics methods within the formalism of density functional theory requires a method to represent the electron wave functions. We compare the use of strictly localized basis functions based on atomic orbitals with the use of plane waves for the study of mineral properties and behaviour. Strictly localized functions enable the computational resources to scale linearly with the size of the system, whereas plane-wave methods scale more as the cube power of the system size, and for this reason the use of localized functions will be preferred for studies of large sizes. We present test results obtained from studies of cation ordering in spinel, garnet and amphibole phases, the high-pressure displacive phase transition in cristobalite, and the intercalation of organic molecules into pyrophyllite. We conclude that the use of localized basis sets provides a useful route forward for quantum mechanical studies of large-scale mineral problems.