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The synthesis of novel organic prototypes combining different functionalities is key to achieve operational elements for applications in organic electronics. Here we set the stage towards individually addressable magneto-optical transducers by the on-surface synthesis of optically active manganese-phthalocyanine derivatives (MnPc) obtained directly on a metallic substrate. We created these 2D nanostructures under ultra-high vacuum conditions with atomic precision starting from a simple phthalonitrile precursor with reversible photo-induced reactivity in solution. These precursors maintain their integrity after powder sublimation and coordinate with the Mn ions into tetrameric complexes and then transform into MnPcs on Ag(111) after a cyclotetramerization reaction. Using scanning tunnelling microscopy and spectroscopy together with DFT calculations, we identify the isomeric configuration of two bi-stable structures and show that it is possible to switch them reversibly by mechanical manipulation. Moreover, the robust magnetic moment brought by the central Mn ion provides a feasible pathway towards magneto-optical transducer fabrication. This work should trigger further research confirming such magneto-optical effects in MnPcs both on surfaces and in liquid environments., We gratefully acknowledge financial support from the Spanish Ministries of Economy, Industry and Competitiveness (MINECO, grants MAT2016-78293-C6-4-R and MAT2016-78293-C6-6) and of Science and Innovation (MICINN, grant no. PID2019-107338RB-C62, PID2019-107338RB-C64, PID2019-107338RB-C66/AEI/10.13039/501100011033 and RED2018-102833-T), the regional Governments of Aragon (E13-20R and E12-20R), the Xunta de Galicia (Centro de Investigación de Galicia acreditation 2019–2022, ED431G 2019/03), the Dept. of Education of the Basque Government and UPV/EHU (grant no. IT1246-19), the Spanish Research Agency (AEI), the European Regional Development Fund (ERDF) under the program Interreg V-A España-Francia-Andorra (contract no. EFA194/16 TNSI) and the European Union through Horizon 2020 (FET-Open project SPRING grant. no. 863098)., We acknowledge support of the publication fee by the CSIC Open Access Publication Support Initiative through its Unit of Information Resources for Research (URICI).

Combining on-surface synthetic methods with the power of scanning tunneling microscopy to characterize novel materials at the single molecule level, we show how to steer the reactivity of one anthracene-based precursor towards different product nanostructures. Whereas using a Au(111) surface with three-fold symmetry results in the dominant formation of a starphene derivative, the two-fold symmetry of a reconstructed Au(110) surface allows the selective growth of non-benzenoid linear conjugated polymers. We further assess the electronic properties of each of the observed product structures via tunneling spectroscopy and DFT calculations, altogether advancing the synthesis and characterization of molecular structures of notable scientific interest that have been only scarcely investigated to date, as applies both to starphenes and to non-benzenoid conjugated polymers., We acknowledge funding from the European Union's Horizon 2020 programme (Grant Agreement No. 635919 and 863098), from the Spanish Agencia Estatal de Investigación (Grant No. MAT2016-78293-C6, PID2019-107338RB-C63, PID2019-107338RB-C66 and FIS2017-83780-P), Xunta de Galicia (Centro singular de investigación de Galicia, accreditation 2019–2022, ED431G 2009/03), Dep. Educación of the Basque Government and UPV/EHU (Grant No. IT-756-13), and the European Regional Development Fund (ERDF).

The catalytic oxidation of CO on transition metals, such as Pt, is commonly viewed as a sharp transition from the CO-inhibited surface to the active metal, covered with O. However, we find that minor amounts of O are present in the CO-poisoned layer that explain why, surprisingly, CO desorbs at stepped and flat Pt crystal planes at once, regardless of the reaction conditions. Using near-ambient pressure X-ray photoemission and a curved Pt(111) crystal we probe the chemical composition at surfaces with variable step density during the CO oxidation reaction. Analysis of C and O core levels across the curved crystal reveals that, right before light-off, subsurface O builds up within (111) terraces. This is key to trigger the simultaneous ignition of the catalytic reaction at different Pt surfaces: a CO-Pt-O complex is formed that equals the CO chemisorption energy at terraces and steps, leading to the abrupt desorption of poisoning CO from all crystal facets at the same temperature., We acknowledge financial support from the Spanish Ministry of Science and Innovation (Grants MAT-2017-88374-P, PID2019-107338RB-C63, PID2019-107338RB-C66), the Basque Government (Grants IT-1255-19, IT-1246-19), the Knut and Alice Wallenberg foundation (DNR KAW 2015.0058 „Atomistic Design of new Catalysts“) and the Swedish Research Council (DNR 349-2011-6491 „Catalysis on the atomic scale“).

For the layered transition metal dichalcogenide 1T-TaS2, we establish through a unique experimental approach and density functional theory, how ultrafast charge transfer in 1T-TaS2 takes on isotropic three-dimensional character or anisotropic two-dimensional character, depending on the commensurability of the charge density wave phases of 1T-TaS2. The X-ray spectroscopic core-hole-clock method prepares selectively in- and out-of-plane polarized sulfur 3p orbital occupation with respect to the 1T-TaS2 planes and monitors sub-femtosecond wave packet delocalization. Despite being a prototypical two-dimensional material, isotropic three-dimensional charge transfer is found in the commensurate charge density wave phase (CCDW), indicating strong coupling between layers. In contrast, anisotropic two-dimensional charge transfer occurs for the nearly commensurate phase (NCDW). In direct comparison, theory shows that interlayer interaction in the CCDW phase - not layer stacking variations - causes isotropic three-dimensional charge transfer. This is presumably a general mechanism for phase transitions and tailored properties of dichalcogenides with charge density waves., AF acknowledges funding by the Helmholtz Virtual Institute VI 419 and the ERC Advanced Investigator Grant No. 669531 EDAX. NM acknowledges funding by the ERC Advanced Investigator Grant No. 321319 ESUX and support from the Carl Tryggers foundation for Scientifc Research CTS. DS-P and MM acknowledge funding from EU-FP7 project THINFACE (grant No. 607232), Spanish MINECO (grant No. MAT2016-78293-C6-4-R), and Basque Dep.de Educación and UPV/EHU (grant No. IT-756-13).

A nanographene formed by the fusion of 22 benzene rings has been prepared by combining an in-solution Pd-catalyzed cycloaddition reaction and on-surface Au-promoted cyclodehydrogenation. The structure and electronic properties of the resulting three-fold symmetric CH molecule have been characterized by scanning probe microscopy with atomic resolution and corroborated by theoretical modelling., This research was supported by the National Science Center, Poland (2017/26/E/ST3/00855), the EU project PAMS (610446), the Agencia Estatal de Investigacion (MAT2016-78293-C6-3-R, MAT2016-78293-C6-4-R, FIS2017-83780-P and CTQ2016-78157-R), the Xunta de Galicia (Centro singular de investigacion de Galicia, acreditacion 2016-2019, ED431G/09) and the European Regional Development Fund (ERDF). R. Z. acknowledges support received from the National Science Center, Poland (2017/24/T/ST5/00262).

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 injection of spin-polarized electrons across interfaces is central to many technologies, and hence, it is important to understand the main ingredients controlling it. Here, we demonstrate that the spin dependence of ultrafast electron transfer at Ar/Co(0001) and Ar/Fe(110) interfaces is rooted in the details of the spin-split surface band structures. The injection dynamics are particularly sensitive to the sizes (in reciprocal space) of projected electronic band gaps around Γ̅. Our ab initio calculations back that minority electrons are injected significantly faster than majority electrons in line with recently reported experimental injection times. A simple tunnelling model incorporating the spin-dependent gap sizes confirms that this ingredient is crucial to rationalize the experimental results., We acknowledge illuminating discussions with Prof. U. Heinzmann and Prof. P. Feulner, as well as financial support from the EU FP7 programme under Grant Agreement No. 607232 (THINFACE), the Spanish Ministerio de Ciencia, Innovacion y Universidades (Grant. No. MAT2016-78293-C6-4-R and Grant No. PID2019-107338RB-C66) and the Basque Dep. de Educacion and the UPV/EHU (Grant No. IT1246-19).

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.

Graphene nanoribbons (GNRs) and their derivatives attract growing attention due to their excellent electronic and magnetic properties as well as the fine-tuning of such properties that can be obtained by heteroatom substitution and/or edge morphology modification. Here, we introduce graphene nanoribbon derivatives—organometallic hybrids with gold atoms incorporated between the carbon skeleton and side Cl atoms. We show that narrow chlorinated 5-AGNROHs (armchair graphene nanoribbon organometallic hybrids) can be fabricated by on-surface polymerization with omission of the cyclodehydrogenation reaction by a proper choice of tailored molecular precursors. Finally, we describe a route to exchange chlorine atoms connected through gold atoms to the carbon skeleton by hydrogen atom treatment. This is achieved directly on the surface, resulting in perfect unsubstituted hydrogen-terminated GNRs. This will be beneficial in the molecule on-surface processing when the preparation of final unsubstituted hydrocarbon structure is desired., This work was supported by the National Science Center, Poland (2019/35/B/ST5/02666), and the EU Project PAMS (610446). A.G.L., D.S.P., and P.B. acknowledge the Spanish Agencia Estatal de Investigación (Grants MAT2016-78293-C6-4-R, PID2019-107338RB-C66, and FIS2017-83780-P), Dep. Educación of the Basque Government and UPV/EHU (Grant IT-756-13), and the European Union (EU) through Horizon 2020 (FET-Open project SPRING Grant 863098) for support.

Miniaturization of electronic circuits into the single-atom level requires novel approaches to characterize transport properties. Due to its unrivaled precision, scanning probe microscopy is regarded as the method of choice for local characterization of atoms and single molecules supported on surfaces. Here we investigate electronic transport along the anisotropic germanium (001) surface with the use of two-probe scanning tunneling spectroscopy and first-principles transport calculations. We introduce a method for the determination of the transconductance in our two-probe experimental setup and demonstrate how it captures energy-resolved information about electronic transport through the unoccupied surface states. The sequential opening of two transport channels within the quasi-one-dimensional Ge dimer rows in the surface gives rise to two distinct resonances in the transconductance spectroscopic signal, consistent with phase-coherence lengths of up to 50 nm and anisotropic electron propagation. Our work paves the way for the electronic transport characterization of quantum circuits engineered on surfaces., This work was supported by the FP7 FET-ICT “Planar Atomic and Molecular Scale devices” (PAMS) project (funded by the European Commission under contract number 610446), the Polish Ministry for Science and Higher Education from financial resources for science in 2013–2017 granted for an international co-financed project (contract number 2913/7.PR/2013/2) and the Spanish Ministerio de Economía y Competitividad (MINECO) (Grant Numbers MAT2016-78293-C6-4-R and FIS2017-83780-P). M.K. acknowledges financial support received from the Polish Ministry of Science and Higher Education, contract number 0341/IP3/2016/74.

San Sebastian (Donostia in the Basque language) is a beautiful, medium-sized European city of about 200,000 inhabitants located at the heart of the Basque Country, next to the Atlantic Ocean and the Pyrenees. Long known as a tourist and culinary destination, San Sebastian has recently become a city of science and technology, with a strong focus on nanoscience research and characterized by an interdisciplinary approach and the support of intense industrial activity in the region. The San Sebastian nanoscience community has contributed considerably to ACS Nano with more than 100 publications during the past decade, some of which have already had significant impact and are highlighted in this virtual issue. This activity has turned this small point at the Basque coastline into a worldwide “nano”-pole for a variety of focused areas of nanoscience research.

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.

Understanding the mechanisms involved in the covalent attachment of organic molecules to surfaces is a major challenge for nanotechnology and surface science. On the basis of classical organic chemistry mechanistic considerations, key issues such as selectivity and reactivity of the organic adsorbates could be rationalized and exploited for the design of molecular-scale circuits and devices. Here we use tris(benzocyclobutadieno)triphenylene, a singular Y-shaped hydrocarbon containing antiaromatic cyclobutadienoid rings, as a molecular probe to study the reaction of polycyclic conjugated molecules with atomic scale moieties, dangling-bond (DB) dimers on a hydrogen-passivated Ge(001):H surface. By combining molecular design, synthesis, scanning tunneling microscopy and spectroscopy (STM/STS) and computational modeling, we show that the attachment involves a concerted [4+2] cycloaddition reaction that is completely site-selective and fully reversible. This selectivity, governed by the bond alternation induced by the presence of the cyclobutadienoid rings, allows for the control of the orientation of the molecules with respect to the surface DB-patterning. We also demonstrate that by judicious modification of the electronic levels of the polycyclic benzenoid through substituents, the reaction barrier height can be modified. Finally, we show that after deliberate tip-induced covalent bond cleavage, adsorbed molecules can be used to fine tune the electronic states of the DB dimer. This power to engineer deliberately the bonding configuration and electronic properties opens new perspectives for creating prototypical nanoscale circuitry., This work was supported by the FP7 FET-ICT “Planar Atomic and Molecular Scale devices” (PAMS) project (funded by the European Commission under contract no. 610446), by the Polish Ministry for Science and Higher Education from financial resources for science in 2013–2017 granted for an international co-financed project (contract no. 2913/7.PR/2013/2) and by projects CTQ2016-78157-R, MAT2016-78293-C6-3R and MAT2016-78293-C6-4R (AEI/FEDER, UE). EG, DP and DP are grateful for financial support from the Xunta de Galicia (Centro singular de investigación de Galicia accreditation 2016–2019, ED431G/09) and the European Union (European Regional Development Fund-ERDF).

This article is licensed under a Creative Commons Attribution-NonCommercial 3.0 Unported Licence., Dangling bond (DB) arrays on Si(001):H and Ge(001):H surfaces can be patterned with atomic precision and they exhibit complex and rich physics making them interesting from both technological and fundamental perspectives. But their complex behavior often makes scanning tunneling microscopy (STM) images difficult to interpret and simulate. Recently it was shown that low-temperature imaging of unoccupied states of an unpassivated dimer on Ge(001):H results in a symmetric butterfly-like STM pattern, despite that the equilibrium dimer configuration is expected to be a bistable, buckled geometry. Here, based on a thorough characterization of the low-bias switching events, we propose a new imaging model featuring a dynamical two-state rate equation. This model allows us to reproduce the features of the observed symmetric empty-state images which strongly corroborates the idea that the patterns arise due to fast switching events and provides insight into the relation between the tunneling current and switching rates. Our new imaging model is general and can be applied to other systems that exhibit rapid fluctuations during STM experiments., The work is funded by the European Commission under the FP7 FET-ICT “Planar Atomic and Molecular Scale devices” (PAMS) project (Contract No. 610446) and National Science Centre, Poland (2014/15/D/ST3/02975). ME, TF, 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). MK acknowledges financial support received from the Foundation for Polish Science (FNP). RZ acknowledges support received from KNOW (scholarship KNOW/44/SS/RZ/2015)., We acknowledge support by the CSIC Open Access Publication Initiative through its Unit of Information Resources for Research (URICI).

Hydrogen molecules can be trapped in the nanocavity formed by the tip of a scanning tunneling microscope and a metal or molecular surface, and produce sharp inelastic non-linearities in the tunneling spectra. Here, we study the interaction effects of hydrogen in a tunneling junction created over Manganese phthalocyanines molecules in two oxidation states. The effect of hydrogen in the tunneling spectra varies strongly depending on the molecular species, but its force spectrum is fairly independent on the molecular state. We find that in mild tunneling conditions hydrogen-induced forces are weakly attractive during a small range of tip sample distance. The van der Waals interaction shows a maximum value of 140 pN, which faintly depends on electrostatic variations along the surface. These results show that AFM can be employed to resolve the complex interaction landscape of a trapped hydrogen molecule and deduce fainter effects such as molecular deformations or dipolar fields., The research was financially supported by the Spanish Ministerio de Economia y Competitividad, MINECO (Grant FIS 2015-62538-ERC, MAT2016-78293-C6, and the Maria de Maeztu Units of Excellence Programme MDM-2016-0618), the Basque Government (Departamento de Industria, grant no. PI-2015-1-42, and Departamento de Educación and UPV/EHU, grant No. IT-756-13), and the European Regional Development Fund (ERDF).

Control of electron transport through molecular devices is a fundamental step toward design of functional molecular electronics. In this respect, the application of the field-effect transistor principle to molecular junctions appears to be a desirable strategy. Here we study the possibility of mechanically controlling the molecular orbital alignment in self-assembled monolayers via the electrostatic fields originating from dipoles at the metal-molecule interfaces. More specifically, we analyze first-principles simulations of prototype alkanedithiolate and alkanediamine monolayer junctions between Au(111) electrodes as a function of inclination of the molecules in the film. We find that the molecular orbital alignment and hence the low-bias conductance of the junctions, sensitively depends on the interface dipole. The dipole change with molecular tilt is rationalized in terms of two electrostatic effects: (i) the reorientation of a dipole associated with the anchoring group and (ii) a dipole modification arising from charge redistribution due to the metal-molecule bond. The first effect, dominating for the thiolates, is the desired way to gate the junctions by tuning of the molecular tilt. However, the second effect, equally important for the amines, may hamper the mechanical control of the level alignment because it depends on other geometric details than the tilt angle. Our results thus suggest that mechanical gating by tilt is achievable with molecules and anchoring groups with strong intrinsic dipole moments and well-defined binding geometry rather than with interface dipoles associated with weak and flexible metal-molecule bonds., G.F. acknowledges support from the CSIC JAE-predoc program, cofinanced by the European Science Foundation. We also acknowledge the support of the Basque Departamento de Educación and the UPV/EHU (Grant No. IT-756-13), the Spanish Ministerio de Economía y Competitividad (Grant No. FIS2010-19609-CO2-00), and the ETORTEK program funded by the Basque Departamento de Industria and the Diputación Foral de Gipuzkoa.

The correlation between transport properties across subnanometric metallic gaps and the optical response of the system is a complex effect that is determined by the fine atomic-scale details of the junction structure. As experimental advances are progressively accessing transport and optical characterization of smaller nanojunctions, a clear connection between the structural, electronic, and optical properties in these nanocavities is needed. Using ab initio calculations, we present here a study of the simultaneous evolution of the structure and the optical response of a plasmonic junction as the particles forming the cavity, two Na380 clusters, approach and retract. Atomic reorganizations are responsible for a large hysteresis of the plasmonic response of the system, which shows a jump-to-contact instability during the approach process and the formation of an atom-sized neck across the junction during retraction. Our calculations demonstrate that, due to the quantization of the conductance in metal nanocontacts, atomic-scale reconfigurations play a crucial role in determining the optical response of the whole system. We observe abrupt changes in the intensities and spectral positions of the dominating plasmon resonances and find a one-to-one correspondence between these jumps and those of the quantized transport as the neck cross-section diminishes. These results reveal an important connection between transport and optics at the atomic scale, which is at the frontier of current optoelectronics and can drive new options in optical engineering of signals driven by the motion and manipulation of single atoms., We acknowledge financial support from Projects FIS2013-41184-P and MAT2013-46593-C6-2-P from MINECO. M.B., P.K., F.M., and D.S.P. also acknowledge support from the ANR-ORGAVOLT project and the Euroregion Aquitaine-Euskadi program. M.B. acknowledges support from the Departamento de Educacion of the Basque Government through a Ph.D. grant. P.K. acknowledges financial support from the Fellows Gipuzkoa program of the Gipuzkoako Foru Aldundia through the FEDER funding scheme of the European Union. J.A. also acknowledges support from Grant 70NANB15H321, “PLASMOQUANTUM”, from the US Department of Commerce (NIST).

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.

This work is licensed under a Creative Commons Attribution 4.0 International License., We present a combined experimental and theoretical study of the electronic properties of close-spaced dangling-bond (DB) pairs in a hydrogen-passivated Si(001):H p-doped surface. Two types of DB pairs are considered, called >cross> and >line> structures. Our scanning tunneling spectroscopy (STS) data show that, although the spectra taken over different DBs in each pair exhibit a remarkable resemblance, they appear shifted by a constant energy that depends on the DB-pair type. This spontaneous asymmetry persists after repeated STS measurements. By comparison with density functional theory (DFT) calculations, we demonstrate that the magnitude of this shift and the relative position of the STS peaks can be explained by distinct charge states for each DB in the pair. We also explain how the charge state is modified by the presence of the scanning tunneling microscopy (STM) tip and the applied bias. Our results indicate that, using the STM tip, it is possible to control the charge state of individual DBs in complex structures, even if they are in close proximity. This observation might have important consequences for the design of electronic circuits and logic gates based on DBs in passivated silicon surfaces., 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, 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). MK acknowledges financial support received from the Polish National Science Centre for preparation of his PhD dissertation (decision number: DEC-2013/08/T/ST3/00047) and from the Foundation for Polish Science (FNP).

Electromagnetic field localization in nanoantennas is one of the leitmotivs that drives the development of plasmonics. The near-fields in these plasmonic nanoantennas are commonly addressed theoretically within classical frameworks that neglect atomic-scale features. This approach is often appropriate since the irregularities produced at the atomic scale are typically hidden in far-field optical spectroscopies. However, a variety of physical and chemical processes rely on the fine distribution of the local fields at this ultraconfined scale. We use time-dependent density functional theory and perform atomistic quantum mechanical calculations of the optical response of plasmonic nanoparticles, and their dimers, characterized by the presence of crystallographic planes, facets, vertices, and steps. Using sodium clusters as an example, we show that the atomistic details of the nanoparticles morphologies determine the presence of subnanometric near-field hot spots that are further enhanced by the action of the underlying nanometric plasmonic fields. This situation is analogue to a self-similar nanoantenna cascade effect, scaled down to atomic dimensions, and it provides new insights into the limits of field enhancement and confinement, with important implications in the optical resolution of field-enhanced spectroscopies and microscopies., We acknowledge financial support from projects FIS2013-14481-P and MAT2013-46593-C6-2-P from MINECO. M.B., P.K., F.M., and D.S.P. also acknowledge support from the ANR-ORGAVOLT project and the Euroregion Aquitaine-Euskadi program. M.B. acknowledges support from the Departamento de Educacion of the Basque Government through a PhD grant, as well as from Euskampus and the DIPC at the initial stages of this work. R.E. and P.K. acknowledge 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”.

We investigate the scattering of surface electrons by the edges of graphene islands grown on Ni(111). By combining local tunneling spectroscopy and ab initio electronic structure calculations we find that the hybridization between graphene and Ni states results in strongly reflecting graphene edges. Quantum interference patterns formed around the islands reveal a spin-dependent scattering of the Shockley bands of Ni, which we attribute to their distinct coupling to bulk states. Moreover, we find a strong dependence of the scattering amplitude on the atomic structure of the edges, depending on the orbital character and energy of the surface states. © 2014 American Physical Society., We acknowledge support from the Basque Departamento de Educación, UPV/EHU (Grants No. IT-366-07 and No. IT-756-13), the Spanish Ministerio de Ciencia e Innovación (Grants No. FIS2010-19609-C02-00, and No. MAT2010-15659), the ETORTEK program funded by the Basque Departamento de Industria, the European Research Council (StG 203239 NOMAD), and Agència de Gestió d’Ajuts Universitaris i de Recerca (2009 SGR 695). A. M. acknowledges funding from the Ramón y Cajal Fellowship program.

The controlled assembly of metal nanoparticles into macroscopic materials using DNA oligonucleotides has opened new directions of research in nanoscience and nanotechnology. Here, we describe recent ab initio calculations on structural and electronic properties of the subsystems forming these materials: bare and thiol-passivated gold nanoclusters, gold nanowires and fragments of DNA chains. Our results indicate that gold nanoclusters are distorted dramatically by a passivating methylthiol monolayer, that monatomic gold chains are stable in zigzag geometries and that dry acidic λ-DNA is a good insulator. These results provide useful insights towards the complete understanding, design and proper utilization of hybrid DNA-gold nanostructured materials.

Recent advances in both first principles computational methodologies for complex systems and qualitative understanding of the electronic structure of solids now make a real dialogue between theoreticians and experimentalists possible. We discuss how this situation can lead to a fruitful interplay in inorganic solid state chemistry, considering selected examples, such as the structure of gold nanoclusters and nanowires, the absorption of atoms and molecules and growth of thin films on silicon surfaces, understanding the development of some structural modulations in low-dimensional transition metal oxides and bronzes, and the control of the transport properties of hybrid organic–inorganic charge transfer molecular solids.

We present a theoretical study of the electronic and magnetic properties of iron systems in different environments: pure iron systems @dimer, bcc bulk, ~100! surface, and free-standing iron monolayer#, and lowdimensional iron systems deposited on Ag ~100! surface ~monoatomic linear wires, iron monolayer, planar, and three-dimensional clusters!. Electronic and magnetic properties have been calculated using a recently developed total-energy first-principles method based on density-functional theory with numerical atomic orbitals as a basis set for the description of valence electrons and nonlocal pseudopotentials for the atomic core. The Kohn-Sham equations are solved self-consistently within the generalized gradient approximation for the exchange-correlation potential. Tests on the pseudopotential, the basis set, grid spacing, and k sampling are carefully performed. This technique, which has been proved to be very efficient for large nonmagnetic systems, is applied in this paper to calculate electronic and magnetic properties of different iron nanostructures. The results compare well with previous ab initio all-electron calculations and with experimental data. The method predicts the correct trends in the magnetic moments of Fe systems for a great variety of environments and requires a smaller computational effort than other ab initio methods.

Knowledge of the structure of clusters is essential to predict many of their physical and chemical properties. Using a many-body semiempirical Gupta potential (to perform global minimizations), and first-principles density functional calculations (to confirm the energy ordering of the local minima), we have recently found [Phys. Rev. Lett. 81, 1600 (1998)] that there are many intermediate-size disordered gold nanoclusters with energy near or below the lowest-energy ordered structure. This is especially surprising because we studied ''magic'' cluster sizes, for which very compact-ordered structures exist. Here, we show how the analysis of the local stress can be used to understand the physical origin of this amorphization. We find that the compact ordered structures, which are very stable for pair potentials, are destabilized by the tendency of metallic bonds to contract at the surface, because of the decreased coordination. The amorphization is also favored by the relatively low energy associated to bondlength and coordination disorder in metals. Although these are very general properties of metallic bonding, we find that they are especially important in the case of gold, and we predict some general trends in the tendency of metallic clusters towards amorphous structures. (c) 2000 The American Physical Society.

Gold nanoclusters with disordered and ordered structures are obtained as the lowest-energy configurations of the cluster potential energy surface (PES) by unconstrained dynamical and genetic/symbiotic optimization methods using an n-body Gupta potential and first-principle calculations [Phys. Rev. Lett. 81, 1600 (1998)]. In this paper, we report the distribution of lowest-energy minima which characterize the PES of the Au38 cluster, and a comparison of structural and thermal stability properties among several representative isomers is presented. Coexistence among different cluster isomeric structures is observed at temperatures around 250 K. The structure factor calculated from the most stable (lowest-energy) amorphous-like cluster configuration is in better agreement with the X-ray powder-diffraction experimental measurements than those calculated from ordered structures.

Bonding and diffusion of a Ba adatom on a Si(001) surface have been studied using first-principles density-functional calculations. It is found that the favorable bonding site of the adatom is the fourfold site located in the trough between Si dimer rows. The bonding between Ba adatom and the surface is shown to be only slightly ionic in character, with a small charge transfer from Ba to the substrate, and with an important covalent component. The calculated jumping rates show a strongly anisotropic diffusivity of Ba on the surface.

The lowest energy structures of ${\mathrm{Au}}_{n}$ ( $n\phantom{\rule{0ex}{0ex}}=\phantom{\rule{0ex}{0ex}}38,55,75$) nanoclusters are obtained by unconstrained dynamical and genetic-symbiotic optimization methods, using a Gupta $n$-body potential. A set of amorphous structures, nearly degenerate in energy, are found as the most stable configurations. Some crystalline or quasicrystalline isomers are also minima of the cluster potential energy surface with similar energy. First principles calculations using density functional theory confirm these results and give different electronic properties for the ordered and disordered gold cluster isomers.

We report on the theoretical study of laser-assisted attosecond photoemission from metals. The full time-dependent quantum approach reveals the role of the resonant interband and nonresonant surface emission processes in formation of final atto-streaking spectra. The present results explain recent experimental data on magnesium and show that the valence band streaking essentially reflects the respective weight of surface and resonant bulk electron ejection. © 2013 American Physical Society., P.M.E. acknowledges partial support from Basque Departamento de Education, Universidades, e Investigation (Grant No. IT-366-07), CONSOLIDER, and the Spanish Ministerio de Ciencia e Innovación (Grant No. FIS2010-19609-C02-00).

We show that chemically synthesized polycyclic aromatic hydrocarbons (PAHs) exhibit molecular plasmon resonances that are remarkably sensitive to the net charge state of the molecule and the atomic structure of the edges. These molecules can be regarded as nanometer-sized forms of graphene, from which they inherit their high electrical tunability. Specifically, the addition or removal of a single electron switches on/off these molecular plasmons. Our first-principles time-dependent density-functional theory (TDDFT) calculations are in good agreement with a simpler tight-binding approach that can be easily extended to much larger systems. These fundamental insights enable the development of novel plasmonic devices based upon chemically available molecules, which, unlike colloidal or lithographic nanostructures, are free from structural imperfections. We further show a strong interaction between plasmons in neighboring molecules, quantified in significant energy shifts and field enhancement, and enabling molecular-based plasmonic designs. Our findings suggest new paradigms for electro-optical modulation and switching, single-electron detection, and sensing using individual molecules. © 2013 American Chemical Society., This work has been supported in part by the Spanish MICINN (MAT2010-14885, FIS2010-19609-C02-00, and Consolider NanoLight.es), the European Commission (FP7-ICT-2009-4-248909-LIMA and FP7-ICT-2009-4-248855-N4E), and the Etortek program. A.M. acknowledges financial support through FPU from the Spanish MEC. P.K. aknowledges support from the CSIC JAE-doc program, cofinanced by the European Science Foundation. P.N. acknowledges support from the Robert A. Welch Foundation (C-1222) and the Office of Naval Research (N00014-10-1-0989).

Density functional theory calculations have been used to analyze the electronic and magnetic properties of ultrathin zigzag graphene nanoribbons (ZGNRs) with different edge saturations. We have compared a symmetric hydrogen saturation of both edges with an asymmetric saturation in which one of the edges is saturated with sulphur atoms or thiol groups, while the other one is kept hydrogen saturated. The adsorption of such partially thiolated ZGNRs on Au(111) has also been explored. We have considered vertical and tilted adsorption configurations of the ribbons, reminiscent of those found for thiolated organic molecules in self-assembled monolayers (SAM) on gold substrates. We have found that saturation with sulphur atoms or thiol groups removes the corresponding edge state from the Fermi energy and kills the accompanying spin polarization. However, this effect is so local that the electronic and magnetic properties of the mono-hydrogenated edge (H-edge) remain unaffected. Thus, the system develops a spin moment mainly localized at the H-edge. This property is not modified when the partially thiolated ribbon is attached to the gold substrate, and is quite independent of the width of the ribbon. Therefore, the upright adsorption of partially thiolated ZGNRs can be an effective way to decouple the spin-polarized channel provided by the H-edge from an underlying metal substrate. These observations might open a novel route to build spin-filter devices using ZGNRs on gold substrates. This journal is © 2013 the Owner Societies., We acknowledge support from Basque Departamento de Educación, UPV/EHU (Grant No. IT-366-07), the Spanish Ministerio de Educación y Ciencia (Grant No. FIS2010-19609-C02-00), and the ETORTEK research program funded by the Basque Departamento de Industria and the Diputación Foral de Gipuzkoa. PCS acknowledges support by the Diputación Foral de Gipuzkoa and to IKERBASQUE, Basque Foundation for Science (48011, Bilbao, Spain).

D. Stradi et al., Monolayer graphene grown on Ru(0001) surfaces forms a superstructure with periodic modulations in its geometry and electronic structure. The large dimension and inhomogeneous features of this superstructure make its description and subsequent analysis a challenge for theoretical modeling based on density functional theory. In this work, we compare two different approaches to describe the same physical properties of this surface, focusing on the geometry and the electronic states confined at the surface. In the more complex approach, the actual moiré structure is taken into account by means of large unit cells, whereas in the simplest one, the graphene moiré is completely neglected by representing the system as a stretched graphene layer that adapts pseudomorphically to Ru(0001). As shown in previous work, the more complex model provides an accurate description of the existing experimental observations. More interestingly, we show that the simplified stretched models, which are computationally inexpensive, reproduce qualitatively the main features of the surface electronic structure. They also provide a simple and comprehensive picture of the observed electronic structure, thus making them particularly useful for the analysis of these and maybe other complex interfaces. © 2013 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. D.S. acknowledges financial support from the FPI-UAM grant program.

Understanding the magnetic properties of graphenic nanostructures is instrumental in future spintronics applications. These magnetic properties are known to depend crucially on the presence of defects. Here we review our recent theoretical studies using density functional calculations on two types of defects in carbon nanostructures: substitutional doping with transition metals, and sp3-type defects created by covalent functionalization with organic and inorganic molecules. We focus on such defects because they can be used to create and control magnetism in graphene-based materials. Our main results are summarized as follows: 1. Substitutional metal impurities are fully understood using a model based on the hybridization between the d states of the metal atom and the defect levels associated with an unreconstructed D3h carbon vacancy. We identify three different regimes, associated with the occupation of distinct hybridization levels, which determine the magnetic properties obtained with this type of doping. 2. A spin moment of 1.0 μ B is always induced by chemical functionalization when a molecule chemisorbs on a graphene layer via a single C–C (or other weakly polar) covalent bond. The magnetic coupling between adsorbates shows a key dependence on the sublattice adsorption site. This effect is similar to that of H adsorption, however, with universal character. 3. The spin moment of substitutional metal impurities can be controlled using strain. In particular, we show that although Ni substitutionals are nonmagnetic in flat and unstrained graphene, the magnetism of these defects can be activated by applying either uniaxial strain or curvature to the graphene layer.

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.

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.

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.

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).