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We study theoretically electron interference in a Mach-Zehnder-like geometry formed by four zigzag graphene nanoribbons (ZGNRs) arranged in parallel pairs, one on top of the other, such that they form intersection angles of 60º. Depending on the interribbon separation, each intersection can be tuned to act either as an electron beam splitter or as a mirror, enabling tuneable circuitry with interfering pathways. Based on the mean-field Hubbard model and Green's function techniques, we evaluate the electron transport properties of such 8-terminal devices and identify pairs of terminals that are subject to self-interference. We further show that the scattering matrix formalism in the approximation of independent scattering at the four individual junctions provides accurate results as compared with the Green's function description, allowing for a simple interpretation of the interference process between two dominant pathways. This enables us to characterize the device sensitivity to phase shifts from an external magnetic flux according to the Aharonov-Bohm effect as well as from small geometric variations in the two path lengths. The proposed devices could find applications as magnetic field sensors and as detectors of phase shifts induced by local scatterers on the different segments, such as adsorbates, impurities or defects. The setup could also be used to create and study quantum entanglement.

Spin-hosting graphene nanostructures are promising metal-free systems for elementary quantum spintronic devices. Conventionally, spins are protected from quenching by electronic band gaps, which also hinder electronic access to their quantum state. Here, we present a narrow graphene nanoribbon substitutionally doped with boron heteroatoms that combines a metallic character with the presence of localized spin 1/2 states in its interior. The ribbon was fabricated by on-surface synthesis on a Au(111) substrate. Transport measurements through ribbons suspended between the tip and the sample of a scanning tunneling microscope revealed their ballistic behavior, characteristic of metallic nanowires. Conductance spectra show fingerprints of localized spin states in the form of Kondo resonances and inelastic tunneling excitations. Density functional theory rationalizes the metallic character of the graphene nanoribbon due to the partial depopulation of the valence band induced by the boron atoms. The transferred charge builds localized magnetic moments around the boron atoms. The orthogonal symmetry of the spin-hosting state’s and the valence band’s wave functions protects them from mixing, maintaining the spin states localized. The combination of ballistic transport and spin localization into a single graphene nanoribbon offers the perspective of electronically addressing and controlling carbon spins in real device architectures., We gratefully acknowledge financial support from Grants PID2019-107338RB-C61, PID2019-107338RB-C62, PID2019-107338RB-C66, PID2019-110037GB-I00, and PCI2019-111933-2 and the Maria de Maeztu Units of Excellence Program CEX2020-001038-M funded by MCIN/AEI/10.13039/501100011033, the European Regional Development Fund, the European Union (EU) H2020 program through the FET Open project SPRING (Grant Agreement No. 863098), the Xunta de Galicia (Centro de Investigación de Galicia accreditation 2019–2022, ED431G 2019/03), the Dpto. Educación Gobierno Vasco (Grant Nos. PIBA-2020-1-0014, IT1246-19, and IT-1569-22) and the Programa Red Guipuzcoana de Ciencia, Tecnología e Innovación 2021 (Grant No. 2021-CIEN-000070-01. Gipuzkoa Next). The authors acknowledge the financial support received from the IKUR Strategy under the collaboration agreement between Ikerbasque Foundation and DIPC on behalf of the Department of Education of the Basque Government.

This article is part of the JCP Special Topic on Electronic Structure Software., A review of the present status, recent enhancements, and applicability of the SIESTA program is presented. Since its debut in the mid-1990s, SIESTA’s flexibility, efficiency, and free distribution have given advanced materials simulation capabilities to many groups worldwide. The core methodological scheme of SIESTA combines finite-support pseudo-atomic orbitals as basis sets, norm-conserving pseudopotentials, and a realspace grid for the representation of charge density and potentials and the computation of their associated matrix elements. Here, we describe the more recent implementations on top of that core scheme, which include full spin–orbit interaction, non-repeated and multiple-contact ballistic electron transport, density functional theory (DFT)+U and hybrid functionals, time-dependent DFT, novel reduced-scaling solvers, density-functional perturbation theory, efficient van der Waals non-local density functionals, and enhanced molecular-dynamics options. In addition, a substantial effort has been made in enhancing interoperability and interfacing with other codes and utilities, such as WANNIER90 and the second-principles modeling it can be used for, an AiiDA plugin for workflow automatization, interface to Lua for steering SIESTA runs, and various post-processing utilities. SIESTA has also been engaged in the Electronic Structure Library effort from its inception, which has allowed the sharing of various low-level libraries, as well as data standards and support for them, particularly the PSeudopotential Markup Language definition and library for transferable pseudopotentials, and the interface to the ELectronic Structure Infrastructure library of solvers. Code sharing is made easier by the new open-source licensing model of the program. This review also presents examples of application of the capabilities of the code, as well as a view of on-going and future developments., Siesta development was historically supported by different Spanish National Plan projects (Project Nos. MEC-DGES-PB95-0202, MCyT-BFM2000-1312, MEC-BFM2003-03372, FIS2006-12117, FIS2009-12721, FIS2012-37549, FIS2015-64886-P, and RTC-2016-5681-7), the latter one together with Simune Atomistics Ltd. We are thankful for financial support from the Spanish Ministry of Science, Innovation and Universities through Grant No. PGC2018-096955-B. We acknowledge the Severo Ochoa Center of Excellence Program [Grant Nos. SEV-2015-0496 (ICMAB) and SEV-2017-0706 (ICN2)], the GenCat (Grant No. 2017SGR1506), and the European Union MaX Center of Excellence (EU-H2020 Grant No. 824143). P.G.-F. acknowledges support from Ramón y Cajal (Grant No. RyC-2013-12515). J.I.C. acknowledges Grant No. RTI2018-097895-B-C41. R.C. acknowledges the European Union’s Horizon 2020 Research and Innovation Program under Marie Skłodoswka-Curie Grant Agreement No. 665919. D.S.P, P.K., and P.B. acknowledge Grant No. MAT2016-78293-C6, FET-Open No. 863098, and UPV-EHU Grant No. IT1246-19. V. W. Yu was supported by a MolSSI Fellowship (U.S. NSF Award No. 1547580), and V.B. and V.W.Y. were supported by the ELSI Development by the NSF (Award No. 1450280).

We report the energy level alignment evolution of valence and conduction bands of armchair-oriented graphene nanoribbons (aGNR) as their band gap shrinks with increasing width. We use 4,4″-dibromo-para-terphenyl as the molecular precursor on Au(111) to form extended poly-para-phenylene nanowires, which can subsequently be fused sideways to form atomically precise aGNRs of varying widths. We measure the frontier bands by means of scanning tunneling spectroscopy, corroborating that the nanoribbon's band gap is inversely proportional to their width. Interestingly, valence bands are found to show Fermi level pinning as the band gap decreases below a threshold value around 1.7 eV. Such behavior is of critical importance to understand the properties of potential contacts in GNR-based devices. Our measurements further reveal a particularly interesting system for studying Fermi level pinning by modifying an adsorbate's band gap while maintaining an almost unchanged interface chemistry defined by substrate and adsorbate., The project leading to this publication has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 635919), from the European Union FP7 FET-ICT “Planar Atomic and Molecular Scale devices” (PAMS) project (Contract No. 610446), from the Spanish Ministry of Economy, Industry and Competitiveness (MINECO, Grant No. MAT2016-78293-C6), from the Basque Department of Education (PI-2016-1-0027), and from the University of Padova (Grant CPDA154322, Project AMNES).

We report the on-surface synthesis of 7-armchair graphene nanoribbons (7-AGNRs) substituted with nitrile (CN) functional groups. The CN groups are attached to the GNR backbone by modifying the 7-AGNR precursor. Whereas many of these groups survive the on-surface synthesis, the reaction process causes the cleavage of some CN from the ribbon backbone and the on-surface cycloisomerization of few nitriles onto pyridine rings. Scanning tunneling spectroscopy and density functional theory reveal that CN groups behave as very efficient n-dopants, significantly downshifting the bands of the ribbon and introducing deep impurity levels associated with the nitrogen electron lone pairs., This work was supported by FP7 FET-ICT “Planar Atomic and Molecular Scale devices” (PAMS) project (funded by the European Commission under Contract No. 610446), by the Agencia Estatal de Investigacion (Cooperative Grant No. MAT2016-78293 and Grant FIS2015-62538-ERC), the Basque Government (Dep. de Educacion and UPV/EHU, Grant No. IT-756-13, and Dep. Industry, Grant PI_2015_1_42), the Xunta de Galicia (Centro singular de investigacion de Galicia accreditation 2016−2019, ED431G/09), and the European Regional Development Fund (ERDF).

We analyze theoretically four-terminal electronic devices composed of two crossed graphene nanoribbons (GNRs) and show that they can function as beam splitters or mirrors. These features are identified for electrons in the low-energy region where a single valence or conduction band is present. Our modeling is based on p z orbital tight binding with Slater-Koster-type matrix elements fitted to accurately reproduce the low-energy bands from density functional theory calculations. We analyze systematically all devices that can be constructed with either zigzag or armchair GNRs in AA and AB stackings. From Green's function theory the elastic electron transport properties are quantified as a function of the ribbon width. We find that devices composed of relatively narrow zigzag GNRs and AA-stacked armchair GNRs are the most interesting candidates to realize electron beam splitters with a close to 50:50 ratio in the two outgoing terminals. Structures with wider ribbons instead provide electron mirrors, where the electron wave is mostly transferred into the outgoing terminal of the other ribbon, or electron filters where the scattering depends sensitively on the wavelength of the propagating electron. We also test the robustness of these transport properties against variations in the intersection angle, stacking pattern, lattice deformation (uniaxial strain), inter-GNR separation, and electrostatic potential differences between the layers. These generic features show that GNRs are interesting basic components to construct electronic quantum optical setups., This work was supported by the project Spanish Ministerio de Economía y Competitividad (MINECO) through the Grants no. FIS2017-83780-P (Graphene Nanostructures “GRANAS”) and no.MAT2016-78293-C6-4R, the Basque Departamento de Educación through the PhD fellowship no. PRE_2019_2_0218 (S.S.), the University of the Basque Country through the Grant no. IT1246-19, and the European Union (EU) through Horizon 2020 (FET-Open project SPRING Grant no. 863098).

Graphene nanoribbons (GNRs), low-dimensional platforms for carbon-based electronics, show the promising perspective to also incorporate spin polarization in their conjugated electron system. However, magnetism in GNRs is generally associated with localized states around zigzag edges, difficult to fabricate and with high reactivity. Here we demonstrate that magnetism can also be induced away from physical GNR zigzag edges through atomically precise engineering topological defects in its interior. A pair of substitutional boron atoms inserted in the carbon backbone breaks the conjugation of their topological bands and builds two spin-polarized boundary states around them. The spin state was detected in electrical transport measurements through boron-substituted GNRs suspended between the tip and the sample of a scanning tunneling microscope. First-principle simulations find that boron pairs induce a spin 1, which is modified by tuning the spacing between pairs. Our results demonstrate a route to embed spin chains in GNRs, turning them into basic elements of spintronic devices., We gratefully acknowledge financial support from Spanish Agencia Estatal de Investigación (AEI) (MAT2016-78293, PID2019-107338RB, FIS2017-83780-P, and the Maria de Maeztu Units of Excellence Programme MDM-2016-0618), from the European Union (EU) through Horizon 2020 (FET-Open project SPRING Grant. No. 863098), the Basque Departamento de Educación through the PhD fellowship No. PRE_2019_2_0218 (S.S.), the Xunta de Galicia (Centro de Investigación de Galicia accreditation 2019–2022, ED431G 2019/03), the University of the Basque Country (Grant IT1246-19), and the European Regional Development Fund (ERDF). I. P. also thanks Xunta de Galicia and European Union (European Social Fund, ESF) for the award of a predoctoral fellowship

The electronic properties of graphene nanoribbons (GNRs) can be precisely tuned by chemical doping. Here we demonstrate that amino (NH2) functional groups attached at the edges of chiral GNRs (chGNRs) can efficiently gate the chGNRs and lead to the valence band (VB) depopulation on a metallic surface. The NH2-doped chGNRs are grown by on-surface synthesis on Au(111) using functionalized bianthracene precursors. Scanning tunneling spectroscopy resolves that the NH2 groups significantly upshift the bands of chGNRs, causing the Fermi level crossing of the VB onset of chGNRs. Through density functional theory simulations we confirm that the hole-doping behavior is due to an upward shift of the bands induced by the edge NH2 groups., We acknowledge financial support from (i) AEI/FEDER-EU through grant nos. MAT2016-78293-C6, FIS2017-83780-P AEI/FEDER, EU, the Maria de Maeztu unit of excellence MDM-2016-0618, and the Severo Ochoa program (ICN2) SEV-2017-0706; (ii) the European Research Council (grant agreement no. 635919); (iii) the Xunta de Galicia (Centro Singular De Investigacion de Galicia, accreditation 2016-2019, ED431G/09); (iv) the European FET-OPEN project SPRING (#863098); (v) the European Regional Development Fund (ERDF) under the program Interreg V-A España-Francia-Andorra (contract no. EFA 194/16 TNI); (vi) the CERCA Program/Generalitat de Catalunya; (vii) the Gobierno Vasco UPV/EHU (project IT1246-19); (viii) Basque Government Project (IT-1255-19); and (ix) Diputacion Foral De Gipuzkoa RED 2019-096.

The evolution of titanyl-phthalocyanine (TiOPc) thin films on Ag(111) has been investigated using IRAS (infrared absorption spectroscopy), SPA-LEED (low energy electron diffraction) and STM (scanning tunneling microscopy). In the (sub)monolayer regime various phases are observed that can be assigned to a 2D gas, a commensurate and a point-on-line phase. In all three phases the nonplanar TiOPc molecule is adsorbed on Ag(111) in an oxygen-up configuration with the molecular π-conjugated backbone oriented parallel to the surface. The commensurate phase reveals a high packing density, containing two molecules at inequivalent adsorption sites within the unit cell. Both molecules assume different azimuthal orientations with respect to the Ag(111) substrate which is ascribed to the interplay between the occupation of preferred sites as well as distinct azimuthal orientations and a short ranging Pauli-Type repulsion to avoid overlapping of neighboring molecules. At full saturation of the monolayer the latter interaction leads to a further azimuthal reorientation that enables an even higher packing density. Thereby, the plain commensurate order is lost and a point-on-line phase is formed. DFT calculations have been used to study different adsorption geometries of TiOPc on Ag(111). The most stable configurations among those with pointing up oxygen atoms (bridge+, bridgex, topx) seem to correspond to those identified experimentally. The calculated dependence of the electronic structure and molecular dipole on the adsorption site and configuration is found to be rather small., We gratefully acknowledge support from the Deutsche Forschungsgemeinschaft DFG (Germany) through the collaborative research center “Structure and Dynamics of Internal Interfaces’’ (SFB 1083, Projects A2, A3, and GP1). DSP acknowledges support from the Spanish MINECO (Grant No. MAT2013-46593-C6-2-P), the Basque Departamento de Educacion, and the UPV/EHU (Grant No. IT-756-13).

We extensively characterize the electronic structure of ultranarrow graphene nanoribbons (GNRs) with armchair edges and zigzag termini that have five carbon atoms across their width (5-AGNRs), as synthesized on Au(111). Scanning tunneling spectroscopy measurements on the ribbons, recorded on both the metallic substrate and a decoupling NaCl layer, show well-defined dispersive bands and in-gap states. In combination with theoretical calculations, we show how these in-gap states are topological in nature and localized at the zigzag termini of the nanoribbons. In addition to rationalizing the driving force behind the topological class selection of 5-AGNRs, we also uncover the length-dependent behavior of these end states which transition from singly occupied spin-split states to a closed-shell form as the ribbons become shorter. Finally, we demonstrate the magnetic character of the end states via transport experiments in a model two-terminal device structure in which the ribbons are suspended between the scanning probe and the substrate that both act as leads., We acknowledge funding from the European Union’s Horizon 2020 programme (Grant Agreement Nos. 635919 and 863098 from ERC and FET Open projects, respectively), from the Spanish MINECO (Grant Nos. FIS2017-83780-P and MAT2016-78293-C6), and from the University of the Basque Country (Grant IT1246-19). D.G.O. thanks the Alexander von Humboldt Foundation for supporting his research stay at the MPI, and Klaus Kern for hosting him.

This article is part of themed collection: 2015 Hot Papers in Nanoscale.-- arXiv:1412.7698v1.-- et al., We present a quantitative exploration, combining experiment and simulation, of the mechanical and electronic properties, as well as the modifications induced by an alkylthiolated coating, at the single nanoparticle (NP) level. We determined the response of the NPs to external pressure in a controlled manner using an atomic force microscope tip. We found a strong reduction in their Young's modulus, as compared to bulk gold, and a significant influence of strain on the electronic properties of the alkylthiolated NPs. Electron transport measurements of tiny molecular junctions (NP/alkylthiol/CAFM tip) show that the effective tunnelling barrier through the adsorbed monolayer strongly decreases by increasing the applied load, which translates in a remarkable and unprecedented increase in the tunnel current. These observations are successfully explained using simulations based on the finite element analysis (FEA) and first-principles calculations that permit one to consider the coupling between the mechanical response of the system and the electric dipole variations at the interface., P.L. is a Senior Research Associate from the Fund for Scientific Research of Belgium (F.R.S. – FNRS). K.S. has been supported by the NordPas-de Calais Council fund and the ANR project SAGE III-V (no. ANR11BS1001203) and S.D. by EU project I-ONE (FP7 no. 280772). The experiments were partly funded by the SINGLEMOL project supported by the Nord-Pas-de Calais council fund. We also acknowledge funding from the Basque Government (Grant No. IT-756-13) and the Spanish MINECO (Grant Nos. MAT2013-46593-C6-2-P and FIS2013-48286-C2-2-P).

Scattering of electrons by localized spins is the ultimate process enabling detection and control of the magnetic state of a spin-doped material. At the molecular scale, scattering is mediated by the orbitals hosting the spin. Here we report the selective excitation of a molecular spin by tunneling through different molecular orbitals. Spatially resolved tunneling spectra on iron-porphyrins reveal that the inelastic spin excitation extends beyond the iron site, changing shape and symmetry along the molecule. Combining density functional theory simulations with a phenomenological scattering model, we show that the extension and lineshape of the inelastic signal are due to excitation pathways assisted by different frontier orbitals. By selecting the intramolecular site for electron injection, the relative weight of iron and pyrrole orbitals in the tunneling process is modified. Thus, the excitation mechanism, reflected by its spectral lineshape, depends on the degree of localization and energy alignment of the chosen molecular orbital., This work has been funded by the COST 15128 Molecular Spintronics project, by Marie Curie IF ARTE, by the Spanish Ministerio de Economía y Competitividad (MINECO) through the cooperative grant No. MAT2016-78293 and grant No. FIS2016-75862-P, and by the Basque Government (Dep. Industry, Grant PI-2015-1-42, Dep. Education, Grant PI-2016-1-27 and Grant IT-756-13), the EU project PAMS (610446), and the European Regional Development Fund (ERDF).

Graphene nanoribbons (GNRs) are promising components in future nanoelectronics due to the large mobility of graphene electrons and their tunable electronic band gap in combination with recent experimental developments of on-surface chemistry strategies for their growth. Here, we explore a prototype 4-terminal semiconducting device formed by two crossed armchair GNRs (AGNRs) using state-of-the-art first-principles transport methods. We analyze in detail the roles of intersection angle, stacking order, inter-GNR separation, GNR width, and finite voltages on the transport characteristics. Interestingly, when the AGNRs intersect at θ=60°, electrons injected from one terminal can be split into two outgoing waves with a tunable ratio around 50% and with almost negligible back-reflection. The split electron wave is found to propagate partly straight across the intersection region in one ribbon and partly in one direction of the other ribbon, i.e., in analogy with an optical beam splitter. Our simulations further identify realistic conditions for which this semiconducting device can act as a mechanically controllable electronic beam splitter with possible applications in carbon-based quantum electronic circuits and electron optics. We rationalize our findings with a simple model suggesting that electronic beam splitters can generally be realized with crossed GNRs., The authors acknowledge financial support from FP7 FET-ICT “Planar Atomic and Molecular Scale devices” (PAMS) project (funded by the European Commission under Contract No. 610446), the Spanish Ministerio de Economia y Competitividad (MINECO) (Grant No. MAT2013-46593-C6-2-P), the Basque Departamento de Educacion, and the UPV/EHU (Grant No. IT-756-13). N.P. acknowledges financial support from No. EU H2020 Project No. 676598, “MaX: Materials at the eXascale” Center of Excellence in Supercomputing Applications.

The theoretical modeling of metal-organic interfaces represents a formidable challenge, especially considering the delicate balance of various interaction mechanisms and the large size of the involved molecular species. In the present study, the energies of interface states, which are known to display a high sensitivity to the adsorption geometry and electronic structure of the deposited molecular species, have been used to test the suitability and reliability of current theoretical approaches. Two well-ordered overlayer structures (relaxed and compressed monolayers) of 1,4,5,8-naphthalene-tetracarboxylic acid dianhydride (NTCDA) on Ag(111) have been investigated using two-photon photoemission to derive precise interface-state energies for these closely related systems. The experimental values are reproduced by our density-functional theory (DFT) calculations with two approaches to treat dispersion interactions (semi-empirical correction DFT-D3 and parametrized functional optB88) and basis set approaches (localized numerical atomic orbitals, plane waves) with remarkable accuracy. Our results underline the trustworthiness and some of the limitations of current DFT-based methods regarding the description of geometric and electronic properties of metal-organic interfaces., This work is a project of the SFB 1083 “Structure and Dynamics of Internal Interfaces” funded by the Deutsche Forschungsgemeinschaft DFG (Germany). D.S.-P. acknowledges support from the Spanish MINECO (Spain), MAT2013-46593-C6-2-P.

arXiv:1609.03842v1, We have theoretically investigated the electronic properties of neutral and n-doped dangling bond (DB) quasi-one-dimensional structures (lines) in the Si(001):H and Ge(001):H substrates with the aim of identifying atomic-scale interconnects exhibiting metallic conduction for use in on-surface circuitry. Whether neutral or doped, DB lines are prone to suffer geometrical distortions or have magnetic ground states that render them semiconducting. However, from our study we have identified one exception—a dimer row fully stripped of hydrogen passivation. Such a DB-dimer line shows an electronic band structure which is remarkably insensitive to the doping level, and thus, it is possible to manipulate the position of the Fermi level, moving it away from the gap. Transport calculations demonstrate that the metallic conduction in the DB-dimer line can survive thermally induced disorder but is more sensitive to imperfect patterning. In conclusion, the DB-dimer line shows remarkable stability to doping and could serve as a one-dimensional metallic conductor on n-doped samples., This work is funded by the FP7 FET-ICT “Planar Atomic and Molecular Scale devices” (PAMS) project (funded by the European Commission under contract No. 610446). ME, PB, TF, AGL, and DSP also acknowledge support from the Spanish Ministerio de Economía y Competitividad (MINECO) (Grant No. MAT2013-46593-C6-2-P) and the Basque Dep. de Educación and the UPV/EHU (Grant No. IT-756-13).

A combined approach of first-principles density-functional calculations and the systematic cluster-expansion scheme is presented. The dipole, quadrupole, and Coulomb matrix elements obtained from ab initio calculations are used as an input to the microscopic many-body theory of the excitonic optical response. To demonstrate the hybrid approach for a nontrivial semiconductor system, the near-bandgap excitonic optical absorption of rutile TiO2 is computed. Comparison with experiments yields strong evidence that the observed near-bandgap features are due to a dipole-forbidden but quadrupole-allowed 1s-exciton state., 14 pages, 4 figures

arXiv:1512.02104v2, We present a study of the optical response of compact and hollow icosahedral clusters containing up to 868 silver atoms by means of time-dependent density functional theory. We have studied the dependence on size and morphology of both the sharp plasmonic resonance at 3–4 eV (originated mainly from sp-electrons), and the less studied broader feature appearing in the 6–7 eV range (interband transitions). An analysis of the effect of structural relaxations, as well as the choice of exchange correlation functional (local density versus generalised gradient approximations) both in the ground state and optical response calculations is also presented. We have further analysed the role of the different atom layers (surface versus inner layers) and the different orbital symmetries on the absorption cross-section for energies up to 8 eV. We have also studied the dependence on the number of atom layers in hollow structures. Shells formed by a single layer of atoms show a pronounced red shift of the main plasmon resonances that, however, rapidly converge to those of the compact structures as the number of layers is increased. The methods used to obtain these results are also carefully discussed. Our methodology is based on the use of localised basis (atomic orbitals, and atom-centered and dominant-product functions), which bring several computational advantages related to their relatively small size and the sparsity of the resulting matrices. Furthermore, the use of basis sets of atomic orbitals also allows the possibility of extending some of the standard population analysis tools (e.g. Mulliken population analysis) to the realm of optical excitations. Some examples of these analyses are described in the present work., This work is supported, in part, by the ORGAVOLT (ORGAnic solar cell VOLTage by numerical computation) Grant ANR-12-MONU-0014-02 of the French Agence Nationale de la Recherche (ANR) 2012 Programme Modèles Numériques. F Marchesin, P Koval and D Sánchez-Portal acknowledge support from the Deutsche Forschungsgemeinschaft (DFG) through the sfb1083 project, the Spanish mineco MAT2013-46593-C6-2-P project, the Euroregion Aquitaine-Euskadi program and from the Basque Departamento de Educación, upv/ehu (Grant No. IT-756-13). Peter Koval acknowledges financial support from the Fellows Gipuzkoa program of the Gipuzkoako Foru Aldundia through the FEDER funding scheme of the European Union.

Under the terms of the Creative Commons Attribution License 3.0 (CC-BY)., The direction and impact parameter dependence of electronic stopping power, along with its velocity threshold behavior, is investigated in a prototypical small-band-gap semiconductor. We calculate the electronic stopping power of H in Ge, a semiconductor with relatively low packing density, using time-evolving time-dependent density-functional theory. The calculations are carried out in channeling conditions with different impact parameters and in different crystal directions for projectile velocities ranging from 0.05 to 0.6 atomic units. The satisfactory comparison with available experiments supports the results and conclusions beyond experimental reach. The calculated electronic stopping power is found to differ in different crystal directions; however, strong impact parameter dependence is observed only in one of these directions. The distinct velocity threshold observed in experiments is well reproduced, and its nontrivial relation with the band gap follows a perturbation theory argument surprisingly well. This simple model is also successful in explaining why different density functionals give the same threshold even with substantially different band gaps., The financial support from MINECO-Spain through Plan Nacional Grant No. FIS2012-37549-C05-01, FPI Ph.D. Fellowship Grant No. BES-2013-063728, and Grant No. MAT2013-46593-C6-2-P along with the EU Grant “ElectronStopping” in the Marie Curie CIG Program is duly acknowledged. SGIker (UPV/EHU, MICINN, GV/EJ, ERDF and ESF) support is gratefully acknowledged.

We have performed a density functional study of fifteen different structural models of the Si(557)-Au surface reconstruction. Here we present a brief summary of the main structural trends obtained for the more favourable models, focusing afterwards in a detailed description of the atomic structure, electronic properties and, simulated STM images of the most stable model predicted by our calculations. This structure is in very good agreement with that recently proposed from X-ray diffraction measurements by Robinson et al. [Phys. Rev. Lett. 88, (2002) 096194]., Comment: 12 pages, including two figures, in preprint format. Submitted to Surface Science on July 2002 (Proceedings of the ECOSS-21 conference)

Under the terms of the Creative Commons Attribution License 3.0 (CC-BY)., The Bethe-Salpeter equation (BSE) is currently the state of the art in the description of neutral electronic excitations in both solids and large finite systems. It is capable of accurately treating charge-transfer excitations that present difficulties for simpler approaches. We present a local basis set formulation of the BSE for molecules where the optical spectrum is computed with the iterative Haydock recursion scheme, leading to a low computational complexity and memory footprint. Using a variant of the algorithm we can go beyond the Tamm-Dancoff approximation. We rederive the recursion relations for general matrix elements of a resolvent, show how they translate into continued fractions, and study the convergence of the method with the number of recursion coefficients and the role of different terminators. Due to the locality of the basis functions the computational cost of each iteration scales asymptotically as O(N3) with the number of atoms, while the number of iterations typically is much lower than the size of the underlying electron-hole basis. In practice we see that, even for systems with thousands of orbitals, the runtime will be dominated by the O(N2) operation of applying the Coulomb kernel in the atomic orbital representation., We acknowledge support from the Deutsche Forschungsgemeinschaft (DFG) through the SFB 1083 project, the ANR ORGAVOLT project, and the Spanish MINECO MAT2013-46593-C6-2-P project. P.K. acknowledges financial support from the Fellows Gipuzkoa program of the Gipuzkoako Foru Aldundia through the FEDER funding scheme of the European Union, Una manera de hacer Europa. F.F. acknowledges support from the EXTRA programme of the “Universita degli Studi di Milano-Bicocca” and from the Erasmus Placement programme for student mobility.

arXiv:1404.5595v1, We investigate by first-principles simulations the resonant electron-transfer lifetime from the excited state of an organic adsorbate to a semiconductor surface, namely, isonicotinic acid on rutile TiO2(110). The molecule-substrate interaction is described using density functional theory, while the effect of a truly semi-infinite substrate is taken into account by Green's function techniques. Excitonic effects due to the presence of core-excited atoms in the molecule are shown to be instrumental to understand the electron-transfer times measured using the so-called core-hole-clock technique. In particular, for the isonicotinic acid on TiO2(110), we find that the charge injection from the LUMO is quenched, since this state lies within the substrate band gap. We compute the resonant charge-transfer times from LUMO+1 and LUMO+2, and systematically investigate the dependence of the elastic lifetimes of these states on the alignment among adsorbate and substrate states. © 2014 American Chemical Society., We acknowledge support from the MIUR of Italy through PRIN project DSSCX (no. 20104XET32). C.M. thanks CARIPLO Foundation for its support within the PCAM European Doctoral Programme and Pirelli Corimav for his Ph.D. scholarship. D.S.-P. acknowledges support from 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), the ETORTEK program funded by the Basque Departamento de Industria and the Diputación Foral de Guipuzcoa, the EU through the FP7 PAMS project, and the German DFG through SFB 1083.

arXiv:1301.6489, We use time-dependent density functional theory to calculate the energy loss of an antiproton colliding with a small Al cluster previously excited. The velocity of the antiproton is such that non-linear effects in the electronic response of the Al cluster are relevant. We obtain that an antiproton penetrating an excited cluster transfers less energy to the cluster than an antiproton penetrating a ground state cluster. We quantify this difference and analyze it in terms of the cluster excitation spectrum. © 2013 Elsevier Ltd. All rights reserved., NEK acknowledges support from the CSIC JAE-predoc program, co-financed by the European Science Foundation. We also acknowledge the support of the Basque Departamento de Educación and the UPV/EHU (Grant No. IT-366-07), the Spanish Ministerio de Economía y Competitividad (Grant No. FIS2010-19609-CO2-02) and the ETORTEK program funded by the Basque Departamento de Industria and the Diputación Foral de Gipuzkoa.

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.

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.

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).

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.

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 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

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.

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.

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.

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

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 calculation of the inelastic scattering rate of Xe atoms on Cu(111) is presented. We focus on the regimes of low and intermediate velocities, where the energy loss is mainly associated to the excitation of electron–hole pairs in the substrate. We consider trajectories parallel to the surface and restrict ourselves to the Van der Waals contribution. The decay rate is calculated within a self-energy formulation. The effect of the response function of the substrate is studied by comparing the results obtained with two different approaches: the specular reflection model and the random phase approximation. In the latter, the surface is described by a finite slab and the wave functions are obtained from a one-dimensional model potential that describes the main features of the surface electronic structure while correctly retains the image-like asymptotic behaviour. We have also studied the influence of the surface state on the calculation, finding that it represents around 50% of the total probability of electron–hole pairs excitation., This work has been partially funded by the University of the Basque Country under Grant UPV/EHU (9/UPV 00206.215-13639/2001) and Spanish MCyT under Grant (MAT2001-0946). D.S.P. acknowledges support from Spanish CSIC and MCyT under the ‘Ramón y Cajal’ programme.

We report a detailed study of the vibrational properties of BN single-walled nanotubes and of the BN monolayer. Our results have been obtained from a well-established tight-binding model complemented with an electrostatic model to account for the long-range interactions arising from the polar nature of the material and which are not included in the tight-binding model. Our study provides a wealth of data for the BN monolayer and nanotubes, such as phonon band structure, vibrational density of states, elastic constants, etc. For the nanotubes we obtain the behavior of the optically active modes as a function of the structural parameters, and we compare their frequencies with those derived from a zone-folding treatment applied to the phonon frequencies of the BN monolayer, finding general good agreement between the two., This work was supported in part by the Spanish Ministerio de Ciencia y Tecnologia Grant Nos. MAT2001-0946, BFM2000-1312-C02, and BFM2002-03278 and by the Basque Departamento de Educacion, Universidades e Investigacion, and the University of the Basque Country UPV/EHU Grant No. 9/UPV 00206.215-13639/ 2001. D.S.P. acknowledges support from the Spanish Ministerio de Ciencia y Tecnologia and CSIC under the ‘‘Ramon y Cajal’’ program. E.H. thanks the IST project SATURN IST-1999-10593.

The Si(557)-Au surface, containing monatomic Au wires parallel to the steps, has been proposed as an experimental realization of an ideal one-dimensional metal. In fact, recent photoemission experiments on this system (Nature 402, 504 (1999)) found two peaks that were interpreted in terms of the spin-charge separation in a Luttinger liquid. Our first-principles density functional calculations reveal two metallic bands associated with Au-Si bonds, instead of the single band expected from the Au 6s states, providing an alternative explanation for the experimental observations., Comment: 5 pages with 3 postscript figures. Submitted to PRL on May 10th 2001

The electronic structure of an infinite poly-guanine - poly-cytosine DNA molecule in its dry A-helix structure is studied by means of density-functional calculations. An extensive study of 30 nucleic base pairs is performed to validate the method. The electronic energy bands of DNA close to the Fermi level are then analyzed in order to clarify the electron transport properties in this particularly simple DNA realization, probably the best suited candidate for conduction. The energy scale found for the relevant band widths, as compared with the energy fluctuations of vibrational or genetic-sequence origin, makes highly implausible the coherent transport of electrons in this system. The possibility of diffusive transport with sub-nanometer mean free paths is, however, still open. Information for model Hamiltonians for conduction is provided., Comment: 8 pages, 4 figures

The adsorption of C60 on Si(111) has been studied by means of first-principles density functional calculations. A 2x2 adatom surface reconstruction was used to simulate the terraces of the 7x7 reconstruction. The structure of several possible adsorption configurations was optimized using the ab initio atomic forces, finding good candidates for two different adsorption states observed experimentally. While the C60 molecule remains closely spherical, the silicon substrate appears quite soft, especially the adatoms, which move substantially to form extra C-Si bonds, at the expense of breaking Si-Si bonds. The structural relaxation has a much larger effect on the adsorption energies, which strongly depend on the adsorption configuration, than on the charge transfer., 4 pages with 3 postscript figures, to appear in Surf. Science. (proceedings of the European Conference on Surface Science ECOSS-19, Sept 2000)

We have developed and implemented a self-consistent density functional method using standard norm-conserving pseudopotentials and a flexible, numerical LCAO basis set, which includes multiple-zeta and polarization orbitals. Exchange and correlation are treated with the local spin density or generalized gradient approximations. The basis functions and the electron density are projected on a real-space grid, in order to calculate the Hartree and exchange-correlation potentials and matrix elements, with a number of operations that scales linearly with the size of the system. We use a modified energy functional, whose minimization produces orthogonal wavefunctions and the same energy and density as the Kohn-Sham energy functional, without the need of an explicit orthogonalization. Additionally, using localized Wannier-like electron wavefunctions allows the computation time and memory, required to minimize the energy, to also scale linearly with the size of the system. Forces and stresses are also calculated efficiently and accurately, thus allowing structural relaxation and molecular dynamics simulations., Comment: 22 pages, 8 figures

Using first-principles density-functional calculations, gold monatomic wires are found to exhibit a zigzag shape which remains under tension, becoming linear just before breaking. At room temperature they are found to spin, which explains the extremely long apparent interatomic distances shown by electron microscopy. The zigzag structure is stable if the tension is relieved, the wire holding its chainlike shape even as a free-standing cluster. This unexpected metallic-wire stiffness stems from the transverse quantization in the wire, as shown in a simple free electron model., This work was supported by Grants No. DGES PB95-0202, No. DOE 8371494, and No. DEFG 02/96/ER 45439.

A brief review of the SIESTA project is presented in the context of linear-scaling density-functional methods for electronic-structure calculations and molecular-dynamics simulations of systems with a large number of atoms. Applications of the method to different systems are reviewed, including carbon nanotubes, gold nanostructures, adsorbates on silicon surfaces, and nucleic acids. Also, progress in atomic-orbital bases adapted to linear-scaling methodology is presented., Comment: 5 pages + 4 figures, submitted to Proc. Int. Conf. Solid State Spectroscopy (Sept 1999)

We apply first principles calculations to study the opening of single-wall carbon nanotubes (SWNT's) by oxidation. We show that an oxygen rim can stabilize the edge of the open tube. The sublimation of CO$_2$ molecules from the rim with the subsequent closing of the tube changes from endothermic to exothermic as the tube radius increases, within the range of experimental feasible radii. We also obtain the energies for opening the tube at the cap and at the wall, the latter being significantly less favorable., Comment: 4 pages, 3 figures. Submitted to Phys. Rev. B

A study based on ab initio calculations is presented on the estructural, elastic, and vibrational properties of single-wall carbon nanotubes with different radii and chiralities. We use SIESTA, an implementation of pseudopotential-density-functional theory which allows calculations on systems with a large number of atoms per cell. Different quantities like bond distances, Young moduli, Poisson ratio and the frequencies of different phonon branches are monitored versus tube radius. The validity of expectations based on graphite is explored down to small radii, where some deviations appear related to the curvature effects. For the phonon spectra, the results are compared with the predictions of the simple zone-folding approximation. Except for the known defficiencies of this approximation in the low-frequency vibrational regions, it offers quite accurate results, even for relatively small radii., Comment: 13 pages, 7 figures, submitted to Phys. Rev. B (11 Nov. 98)

The projection of the eigenfunctions obtained in standard plane-wave first-principle electronic-structure calculations into atomic-orbital basis sets is proposed as a formal and practical link between the methods based on plane waves and the ones based on atomic orbitals. Given a candidate atomic basis, ({\it i}) its quality is evaluated by its projection into the plane-wave eigenfunctions, ({\it ii}) it is optimized by maximizing that projection, ({\it iii}) the associated tight-binding Hamiltonian and energy bands are obtained, and ({\it iv}) population analysis is performed in a natural way. The proposed method replaces the traditional trial-and-error procedures of finding appropriate atomic bases and the fitting of bands to obtain tight-binding Hamiltonians. Test calculations of some zincblende semiconductors are presented., RevTex. 4 pages. 3 uuencoded compressed (tared) postscript figs. To appear in Solid St. Commun

The projection of the eigenfunctions obtained in standard plane-wave first-principle calculations is used for analyzing atomic-orbital basis sets. The "spilling" defining the error in such a projection allows the evaluation of the quality of an atomic-orbital basis set for a given system and its systematic variational optimization. The same projection allows obtaining the band structure and the Hamiltonian matrix elements in the previously optimized atomic basis. The spilling is shown to correlate with the mean square error in the energy bands, indicating that the basis optimization via spilling minimization is qualitatively equivalent to the energy-minimization scheme, but involves a much smaller computational effort. The spilling minimization also allows the optimization of bases for uses different than total-energy calculations, like the description of the band gap in semiconductors. The method is applied to the characterization of finite-range pseudo-atomic orbitals {[}O. F. Sankey and D. J. Niklewski, Phys. Rev. B {\bf 40}, 3979 (1989){]} in comparison to infinite-range pseudo-atomic and Slater-type orbitals. The bases are evaluated and optimized for several zincblende semiconductors and for aluminum. The quality of the finite-range orbitals is found to be perfectly comparable to the others with the advantage of a limited range of interacions. A simple scheme is proposed to expand the basis without increasing the range. It is found that a double-$z$ basis substantially improves the basis performance on diamond, whereas $d$-polarization is required for Si and Al for similar results. Finally, the projection allows the chemical analysis of the plane-wave results via population analysis on the previously optimized atomic basis., Comment: 11 pages, RevTeX, plus 13 uuencoded, compressed, tared figures

This is an Open Access article distributed under the terms of the Creative Commons Attribution License.-- This article is part of the series 12th Trends in NanoTechnology International Conference (TNT2011)., Recent advances in attosecond spectroscopy techniques have fueled the interest in the theoretical description of electronic processes taking place in the subfemtosecond time scale. Here we study the coupled dynamic screening of a localized hole and a photoelectron emitted from a metal cluster using a semi-classical model. Electron density dynamics in the cluster is calculated with Time-Dependent Density Functional Theory and the motion of the photoemitted electron is described classically. We show that the dynamic screening of the hole by the cluster electrons affects the motion of the photoemitted electron. At the very beginning of its trajectory, the photoemitted electron interacts with the cluster electrons that pile up to screen the hole. Within our model, this gives rise to a significant reduction of the energy lost by the photoelectron. Thus, this is a velocity dependent effect that should be accounted for when calculating the average losses suffered by photoemitted electrons in metals., NEK acknowledges support from the CSIC JAE-predoc program, co-financed by the European Science Foundation. We also acknowledge the support of the Basque Departamento de Educación and the UPV/EHU (Grant No. IT-366-07), the Spanish Ministerio de Economía y Competitividad (Grant No. FIS2010-19609-CO2-02) and the ETORTEK program funded by the Basque Departamento de Industria and the Diputación Foral de Gipuzkoa.

arXiv:1203.2111, The transmission properties of armchair graphene nanoribbon junctions between graphene electrodes are investigated by means of first-principles quantum transport calculations. First the dependence of the transmission function on the size of the nanoribbon has been studied. Two regimes are highlighted: for a small applied bias transport takes place via tunneling and the length of the ribbon is the key parameter that determines the junction conductance; at a higher applied bias resonant transport through the HOMO and LUMO starts to play a more determinant role, and the transport properties depend on the details of the geometry (width and length) of the carbon nanoribbon. In the case of the thinnest ribbon it has been verified that a tilted geometry of the central phenyl ring is the most stable configuration. As a consequence of this rotation the conductance decreases due to the misalignment of the π orbitals between the phenyl ring and the remaining part of the junction. All the computed transmission functions have shown a negligible dependence on different saturations and reconstructions of the edges of the graphene leads, suggesting a general validity of the reported results. © 2012 the Owner Societies., C.M. thanks the CARIPLO Foundation for its support within the PCAM European Doctoral Programme and Pirelli-Corimav. D.S.P. acknowledges support from 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 research program funded by the Basque Departamento de Industria and the Diputación Foral de Gipuzkoa.

We investigate the electronic structure of carbon nanotubes functionalized by adsorbates anchored with single C-C covalent bonds. We find that, despite the particular adsorbate, a spin moment with a universal value of 1.0 $\mu_B$ per molecule is induced at low coverage. Therefore, we propose a mechanism of bonding-induced magnetism at the carbon surface. The adsorption of a single molecule creates a dispersionless defect state at the Fermi energy, which is mainly localized in the carbon wall and presents a small contribution from the adsorbate. This universal spin moment is fairly independent of the coverage as long as all the molecules occupy the same graphenic sublattice. The magnetic coupling between adsorbates is also studied and reveals a key dependence on the graphenic sublattice adsorption site., Comment: final version, improved discussion about calculations and defect concentration