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The intermolecular interaction among phthalocyanine molecules deposited on Ag(111) has been investigated at submonolayer coverages. By means of infrared absorption spectroscopy and spot-profile analysis low-energy electron diffraction, unambiguous evidence for an attractive interaction between neighboring titanyl-phthalocyanine (TiOPc) molecules is found for dilute layers, which is in contrast to the intermolecular repulsion reported for the copper-phthalocyanine (CuPc)/Ag(111) system. Accordingly, the formation of dense two-dimensional islands of TiOPc molecules with a well-defined long-range order (commensurate phase) is observed upon cooling to temperatures below 75 K, while a disordered arrangement is retained for adsorbed CuPc. Using density functional theory (DFT) calculations as a guide, these differences have been traced to the competition of attractive van der Waals and repulsive electrostatic interactions. Specifically, the vertically oriented molecular dipoles are substantially smaller for adsorbed TiOPc as compared to CuPc due to a compensation of the oppositely oriented dipole moments arising from the Pauli push-back effect on the one hand and the internal molecular dipole associated with the axial Ti–O group on the other. A detailed account and comparison of the molecule–substrate interaction, molecular binding geometries, and intermolecular interactions of TiOPc and CuPc on the Ag(111) surface are provided in a theoretical analysis based on DFT., We gratefully acknowledge support from the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation), Project ID 223848855-SFB 1083 “Structure and Dynamics of Internal Interfaces”. L.F. acknowledges financial support from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement MagicFACE no. 797109. D.S.-P. and A.X.B.-R. acknowledge the Spanish Agencia Estatal de Investigación (grant nos. MAT2016-78293-C6-4-R and PID2019-107338RB-C66) and Dep. Educación of the Basque Government and UPV/EHU (grant no. IT1246-19) for support.

A prerequisite to characterize magnetic materials is the capability to describe systems containing unpaired electrons. In this study, we benchmark the one-shot GW (G0W0) on top of different unrestricted mean-field solutions for open-shell molecules using Dunning's correlation-consistent basis sets expanded in terms of Gaussian functions. We find that the G0W0 correction to hybrid functionals provides reasonably accurate results for the ionization energies of open-shell systems when compared to those obtained from high-level ab initio methods. Moreover, the quality of the G0W0 exchange–correlation approximation is evaluated by the discrepancy between the ionization energy of the neutral molecules and the electron affinity of the corresponding cations. Furthermore, we assess the capability of the GW to reproduce the correct energy ordering of molecular spin–orbitals. To such an aim, we thoroughly discuss three open-shell molecules CN, NH2, and O2, for which approximate functionals fail to correctly capture the single-electron spectrum. Particularly, we demonstrate that the overestimation of the exchange energy in the studied spin–orbitals is reduced by the GW dynamic correlation term, restoring the molecular orbital ordering. Interestingly, we find that deviations of the exchange and correlation energies, in comparison with our ab initio reference, can be very different for molecular orbitals with different symmetry, e.g. σ and π-type orbitals., Authors acknowledge support from Spanish Agencia Estatal de Investigación (Grant Nos. PID2019-107338RB-C66, PID2019-109555GB-I00 and RTC-2016-5681-7), and the Eusko Jaurlaritza and UPV/EHU (Grant Nos. PIBA19-0004 and IT1246-19). DSP also acknowledges support from the European Union (EU) through Horizon 2020 (FET-Open project SPRING Grant No. 863098).

By means of spin-resolved density functional theory calculations using both atomic orbitals and plane-wave basis codes, we study the electronic and magnetic ground state of single-layer NbSe2. We find that, for all the functionals considered, the most stable solution in this two-dimensional (2D) superconductor is the ferrimagnetic ground state with a magnetic moment of 1.09 μB at the Nb atoms and of 0.05 μB at the Se atoms pointing in the opposite direction. Our calculations show that the ferrimagnetic state precludes the development of charge density wave (CDW) order and their coexistence in the single-layer limit, unless graphene is considered as a substrate. The spin-resolved calculated density of states (DOS), a key fingerprint of the electronic and magnetic structure of a material, unambiguously reproduces the experimental DOS measured by scanning tunneling spectroscopy in single-layer NbSe2. Our work sets magnetism into play in this prototypical correlated 2D material, which is crucial to understand the formation mechanisms of 2D superconductivity and CDW order., We are indebted to Spanish Ministry of Science and Innovation for financial support through Grant FIS2015-64886-C5-5-P and MAT2017-83553-P. MMU acknowledges support by the Spanish MINECO under Grant No. MAT2017-88377-C2-1-R and by the ERC Starting Grant LINKSPM (Grant 758558). EB acknowledges support from the Scientific and Technological Research Council of Turkey (TUBİTAK) under Grant No. 1059B141801387 and DSP from Spanish Ministry of Science and Innovation under Grant PID2019-107338RB-C66.

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).

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“).

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.

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.

The use of atomic orbitals in Hedin's GW approximation provides, in principle, an inexpensive alternative to plane-wave basis sets, especially when modeling large molecules. However, benchmarking of the algorithms and basis sets is essential for a careful balance between cost and accuracy. In this paper, we present an implementation of the GW approximation using numerical atomic orbitals and a pseudopotential treatment of core electrons. The combination of a contour deformation technique with a one-shot extraction of quasiparticle energies provides an efficient scheme for many applications. The performance of the implementation with respect to the basis set convergence and the effect of the use of pseudopotentials has been tested for the 117 closed-shell molecules from the G2/97 test set and 24 larger acceptor molecules from another recently proposed test set. Moreover, to demonstrate the potential of our method, we compute the thermally averaged GW density of states of a large photochromic compound by sampling ab initio molecular dynamics trajectories at different temperatures. The computed thermal line widths indicate approximately twice as large electron-phonon couplings with GW than with standard DFT-GGA calculations. This is further confirmed using frozen-phonon calculations.

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).

Plasmonic gaps are known to produce nanoscale localization and enhancement of optical fields, providing small effective mode volumes of about a few hundred nm. Atomistic quantum calculations based on time-dependent density functional theory reveal the effect of subnanometric localization of electromagnetic fields due to the presence of atomic-scale features at the interfaces of plasmonic gaps. Using a classical model, we explain this as a nonresonant lightning rod effect at the atomic scale that produces an extra enhancement over that of the plasmonic background. The near-field distribution of atomic-scale hot spots around atomic features is robust against dynamical screening and spill-out effects and follows the potential landscape determined by the electron density around the atomic sites. A detailed comparison of the field distribution around atomic hot spots from full quantum atomistic calculations and from the local classical approach considering the geometrical profile of the atoms' electronic density validates the use of a classical framework to determine the effective mode volume in these extreme subnanometric optical cavities. This finding is of practical importance for the community of surface-enhanced molecular spectroscopy and quantum nanophotonics, as it provides an adequate description of the local electromagnetic fields around atomic-scale features with use of simplified classical methods., Financial support from Project No. FIS2016-80174-P and MAT2016-78293-C6-4-R of MINECO, grant of Consolidated Groups at UPV/EHU (IT-756-13) of the Basque Government, and project 70NANB15H32 from U.S. Department of Commerce, National Institute of Standards and Technology, is acknowledged. M.U. acknowledges support from the University of the Basque Country through a Ph.D. grant, as well as DIPC and CFM at the initial stages of this work. M.B. acknowledges support from the Departamento de Educacion of the Basque Government through a Ph.D. grant, as well as from Euskampus and the DIPC at the initial stages of this work. 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”.

We present an algorithm and its implementation to calculate the properties of electronic excitations in molecules and clusters from first principles, using time-dependent density functional theory (TDDFT). The algorithm assumes the use of some localized functions as a basis set to represent the spatial degrees of freedom. It relies on an iterative computation of the induced density according to the Dyson-like equation for the linear response function. The current implementation is built upon so-called numerical atomic orbitals. It is suitable for a wide variety of density functional theory (DFT) software. In this work, we demonstrate TDDFT calculations starting from preceding DFT runs with SIESTA, GPAW and PySCF packages, while a coupling with the other DFT packages such as Fireball and OpenMX is planned. The mentioned packages are capable of performing ab initio molecular dynamics simulations, and the speed of our TDDFT implementation makes feasible to perform a configuration average of the optical absorption spectra. Our code is written mostly in Python language allowing for a quick and compact implementation of most numerical methods and data-managing tasks with the help of NumPy/SciPy libraries and Python intrinsic constructs. Part of the code is written in C and Fortran to achieve a competitive speed in particular sections of the algorithm. Many parts of the current algorithm and implementation are useful in other ab initio methods for electronic excited states, such as Hedin¿s GW, Bethe¿Salpeter equation and DFT with hybrid functionals. Corresponding proof-of-principles implementations are already part of the code., PK and DSP acknowledge support from Spanish MINECO Grants MAT2016-78293-C6-4-R and RTC-2016-5681-7 (SIESTA-PRO). PKacknowledges financial support from the Fellows Gipuzkoa program of the Gipuzkoako Foru Aldundia through the FEDER fundings cheme of the European Union.MB acknowledges support from the Departemento de Educación of the Basque Government through aPhD grant, as well as from Euskampus and the DIPC at the initial stages of this work

This work was partially supported by the Basque Departamento de Educacion, Universidades e Investigacion, the University of the Basque Country UPV/EHU (Grant No. IT-756-13) and the Spanish Ministerio de Economia y Competitividad (Grants No. FIS2016-76471-P and No. MAT2016-78293-C6-4-R). We are indebted to the Brazilian agencies CAPES, CNPq, and FAPERGS for partial support of the experimental part of this work.

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).

Pentacene molecules have recently been observed to form a well-ordered monolayer on the (110) surface of rutile TiO, with the molecules adsorbed lying flat, head to tail. With the geometry favorable for direct optical excitation and given its ordered character, this interface seems to provide an intriguing model to study charge-transfer excitations where the optically excited electrons and holes reside on different sides of the organic-inorganic interface. In this work, we theoretically investigate the structural and electronic properties of this system by means of ab initio calculations and compute its excitonic absorption spectrum. Molecular states appear in the band gap of the clean TiO surface, which enables charge-transfer excitations directly from the molecular HOMO to the TiO conduction band. The calculated optical spectrum shows a strong polarization dependence and displays excitonic resonances corresponding to the charge-transfer states, which could stimulate new experimental work on the optical response of this interface., This work was financed by the Deutsche Forschungsgemeinschaft (DFG) through the SFB 1083 project. MPL, DSP and PK also acknowledges support from Spanish MINECO (Grants No. MAT2013-46593-C6-2-P and MAT2016-78293-C6-4-R) and PK also acknowledges financial support from Fellows Guipuzcoa program from Gipuzkoako Foru Aldundia through the FEDER funding scheme of the European Union.

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 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).

et al., A vicinal rutile TiO(110) crystal with a smooth variation of atomic steps parallel to the [1-10] direction was analyzed locally with STM and ARPES. The step edge morphology changes across the samples, from [1-11] zigzag faceting to straight [1-10] steps. A step-bunching phase is attributed to an optimal (110) terrace width, where all bridge-bonded O atom vacancies (O vacs) vanish. The [1-10] steps terminate with a pair of 2-fold coordinated O atoms, which give rise to bright, triangular protrusions (S) in STM. The intensity of the Ti 3d-derived gap state correlates with the sum of O vacs plus S protrusions at steps, suggesting that both O vacs and steps contribute a similar effective charge to sample doping. The binding energy of the gap state shifts when going from the flat (110) surface toward densely stepped planes, pointing to differences in the Ti polaron near steps and at terraces., We acknowledge financial support from the Spanish Ministry of Economy (Grants MAT2013-46593-C6-4-P and MAT2013-46593-C6-2-P) and the Basque Government (Grant IT621-13 and IT756-13). M.S. and U.D. acknowledge support from the ERC Advanced Grant “OxideSurfaces”. D.S.P. and M.M. acknowledge support from the Marie Curie ITN “THINFACE” and financial support by the Deutsche Forschungsgemeinschaft. through SFB 1083 “Structure and Dynamics of Internal Interfaces”.

Controlling the strength of the coupling between organic molecules and single atoms provides a powerful tool for tuning electronic properties of single-molecule devices. Here, using scanning tunneling microscopy and spectroscopy (STM/STS) supported by theoretical modeling, we study the interaction of a planar organic molecule (trinaphthylene) with a hydrogen-passivated Ge(001):H substrate and a single dangling bond quantum dot on that surface. The electronic structure of the molecule adsorbed on the hydrogen-passivated surface is similar to the gas phase structure and the measurements show that HOMO and LUMO states contribute to the STM filled and empty state images, respectively. Furthermore, we show that the electronic properties are not significantly affected when the molecule is attached to the single dangling bond, which is in contrast with the strong interaction of the molecule with a dangling bond dimer. Our results show that the dangling bond quantum dots could stabilize organic molecules on a hydrogenated semiconductor without affecting their originally designed gas phase electronic properties. Together with the ability to laterally manipulate the molecules on the surface, this will be advantageous in the construction of single-molecule devices, where the coupling and positioning of the molecules on the substrate could be tuned by a proper design of the surface quantum dot arrays, comprising both single and dimerized dangling bonds., This work was supported by the Polish Ministry for Science and Higher Education, contract no. 0322/IP3/2013/72. The experiment was carried out using equipment purchased with financial support from the European Regional Development Fund within the framework of the Polish Innovation Economy Operational Program (contract no. POIG.02.01.00-12-023/08). ME, AGL and DSP acknowledge funding by the 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) and the Basque Department of Education and the UPV/EHU (Grant No. IT-756-13). MK acknowledges financial support received from the Foundation for Polish Science (FNP). SG acknowledges the support from the National Science Centre, Poland (2014/15/D/ST3/02975). AME acknowledges the MINECO (Grant No. CTQ2013-42106-P). HK acknowledges the A*STAR Computational Resource Centre (A*CRC) for the computational resources and support. RZ acknowledges support received from KNOW (scholarship KNOW/44/SS/RZ/2015).

Construction of single-molecule electronic devices requires the controlled manipulation of organic molecules and their properties. This could be achieved by tuning the interaction between the molecule and individual atoms by local “on-surface” chemistry, i.e., the controlled formation of chemical bonds between the species. We demonstrate here the reversible attachment of a planar conjugated polyaromatic molecule to a pair of unpassivated dangling bonds on a hydrogenated Ge(001):H surface via a Diels–Alder [4+2] addition using the tip of a scanning tunneling microscope (STM). Due to the small stability difference between the covalently bonded and a nearly undistorted structure attached to the dangling bond dimer by long-range dispersive forces, we show that at cryogenic temperatures the molecule can be switched between both configurations. The reversibility of this covalent bond forming reaction may be applied in the construction of complex circuits containing organic molecules with tunable properties., This work was supported by the National Science Centre, Poland (2014/15/D/ST3/02975). The experiment was carried out using equipment purchased with financial support from the European Regional Development Fund within the framework of the Polish Innovation Economy Operational Program (contract no. POIG.02.01.00-12-023/08). ME, AGL and DSP acknowledge funding by the 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) and the Basque Department of Education and the UPV/EHU (Grant No. IT-756-13). MK acknowledges financial support received from the Foundation for Polish Science (FNP). SG acknowledges the support from the Polish Ministry for Science and Higher Education, contract no. 0322/IP3/2013/72. AME acknowledges the MINECO (Grant No. CTQ2013-42106-P). HK acknowledges the A*STAR Computational Resource Centre (A*CRC) for the computational resources and support. CJ acknowledges the MANA NEXT financial support during this work. RZ acknowledges support received from KNOW (scholarship KNOW/44/SS/RZ/2015).

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).

In a recent study [M. Feng, et al., ACS Nano, 2011, 5, 8877], it was shown that CO molecules adsorbed on the quasi-one-dimensional O(2 × 1)/Cu(110) surface reconstruction tend to form highly-ordered single-molecule-wide rows along the direction perpendicular to the Cu–O chains. This stems from the peculiar tilted adsorption configuration of CO on this substrate, which gives rise to short-range attractive dipole–dipole interactions. Motivated by this observation, here we study the adsorption of nitric oxide (NO) on O(2 × 1)/Cu(110) and Cu(110) using density functional theory, with the aim of elucidating whether a similar behaviour can be expected for this molecule. We first study NO adsorption on a clean Cu(110) surface, where the role of short-range attractions between molecules has already been pointed out by the observation of the formation of NO dimers by scanning tunnelling microscopy [A. Shiotari, et al., Phys. Rev. Lett., 2011, 106, 156104]. On the clean Cu(110), the formation of dimers along the [1[1 with combining macron]0] direction is favourable, in agreement with published experimental results. However, the formation of extended NO rows is found to be unstable. Regarding the O(2 × 1)/Cu(110) substrate, we observe that NO molecules adsorb in between the Cu–O chains, causing a substantial disruption of the surface structure. Although individual molecules can be tilted with negligible energetic cost along the direction of the Cu–O chains, the interaction among neighbouring molecules was found to be repulsive along all directions and, consequently, the formation of dimers unfavourable., The authors acknowledge support from the Spanish Ministerio de Economa y Competitividad (MINECO) (Grant No. MAT2013-46593-C6-2-P), the Basque Departamento de Educación and the UPV/EHU (Grant No. IT-756-13), and the Deutsche Forschungsgemeinschaft through the Sonderforschungsbereich 1083. AXBR acknowledges support from the Basque Departamento de Educación and the UPV/EHU through a Zabalduz grant.

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 article belongs to the Special Issue 50th Anniversary of the Kohn-Sham Theory—Advances in Density Functional Theory., Ionization potentials (IPs) and electron affinities (EAs) are important quantities input into most models for calculating the open-circuit voltage (Voc) of organic solar cells. We assess the semi-empirical density-functional tight-binding (DFTB) method with the third-order self-consistent charge (SCC) correction and the 3ob parameter set (the third-order DFTB (DFTB3) organic and biochemistry parameter set) against experiments (for smaller molecules) and against first-principles GW (Green’s function, G, times the screened potential, W) calculations (for larger molecules of interest in organic electronics) for the calculation of IPs and EAs. Since GW calculations are relatively new for molecules of this size, we have also taken care to validate these calculations against experiments. As expected, DFTB is found to behave very much like density-functional theory (DFT), but with some loss of accuracy in predicting IPs and EAs. For small molecules, the best results were found with ΔSCF (Δ self-consistent field) SCC-DFTB calculations for first IPs (good to ± 0.649 eV). When considering several IPs of the same molecule, it is convenient to use the negative of the orbital energies (which we refer to as Koopmans’ theorem (KT) IPs) as an indication of trends. Linear regression analysis shows that KT SCC-DFTB IPs are nearly as accurate as ΔSCF SCC-DFTB eigenvalues (± 0.852 eV for first IPs, but ± 0.706 eV for all of the IPs considered here) for small molecules. For larger molecules, SCC-DFTB was also the ideal choice with IP/EA errors of ± 0.489/0.740 eV from ΔSCF calculations and of ± 0.326/0.458 eV from (KT) orbital energies. Interestingly, the linear least squares fit for the KT IPs of the larger molecules also proves to have good predictive value for the lower energy KT IPs of smaller molecules, with significant deviations appearing only for IPs of 15–20 eV or larger. We believe that this quantitative analysis of errors in SCC-DFTB IPs and EAs may be of interest to other researchers interested in DFTB investigation of large and complex problems, such as those encountered in organic electronics., 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. Mathias P. Ljungberg, Peter Koval and Daniel Sánchez-Portal acknowledge support from the Deutsche Forschungsgemeinschaft (DFG) through the SFB (Sonderforschungsbereich) 1083 project, the Spanish MINECO (Ministerio de Economía y Competitividad) MAT2013-46593-C6-2-P project and the Euroregion Aquitaine-Euskadi program and support from the Basque Departamento de Educación, UPV/EHU (University of the Basque Country) (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. Ala Aldin M. H. M. Darghouth would like to thank the French and Iraq governments for support through a Campus France scholarship. Walid Taouali would like to acknowledge support from the government of Tunisia.

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).

26th International Conference on Atomic Collisions in Solids, A method is presented to compute the dielectric function for extended systems using linear response time-dependent density functional theory. Localized basis functions with finite support are used to expand both eigenstates and response functions. The electron-energy loss function is directly obtained by an iterative Krylov-subspace method. We apply our method to graphene and silicon and compare it to plane-wave based approaches. Finally, we compute electron-energy loss spectrum of C60 crystal to demonstrate the merits of the method for molecular crystals, where it will be most competitive., We acknowledge support from ANR OrgaVolt project. D.S-P. and P.K. acknowledge 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. D.S-P., P.K. and M.P.L. acknowledge the German DFG through SFB 1083.

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.

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).

(Received 2 December 2011; published 31 May 2012) The electronic stopping power of H and He moving through gold is obtained to high accuracy using time-evolving density-functional theory, thereby bringing usual first principles accuracies into this kind of strongly coupled, continuum nonadiabatic processes in condensed matter. The two key unexplained features of what observed experimentally have been reproduced and understood: (i) The nonlinear behavior of stopping power versus velocity is a gradual crossover as excitations tail into the d-electron spectrum; and (ii) the low-velocity H=He anomaly (the relative stopping powers are contrary to established theory) is explained by the substantial involvement of the d electrons in the screening of the projectile even at the lowest velocities where the energy loss is generated by s-like electron-hole pair formation only.

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.

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.

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).

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

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

We use time dependent density functional theory to study short-time dynamics of the screening of a negative charge suddenly introduced in a free electron gas. The electron gas is modeled with a finite-size jellium cluster. We find that the screening is built-up locally on a time scale well below the femtosecond for typical metallic densities. At this ultrashort time scale, the time evolution is not affected by the cluster boundary conditions, and our results apply to the infinite system as well. The results for different electronic densities can be understood in terms of universal scaling laws. © 2004 Elsevier B.V. All rights reserved., This work was supported in part by the Basque Departamento de Educación, Universidades e Investigación, the University of the Basque Country UPV/ EHU (Grant No. 9/UPV 00206.215-13639/2001), and the Spanish MCyT (Grant No. MAT2001-0946). AB acknowledges financial support from the DIPC, and DSP from the Spanish MCyT and CSIC.

``14-1-11'' phase compounds, based on magnetic Mn ions and typified by ${\mathrm{Ca}}_{14}{\mathrm{MnBi}}_{11}$ and ${\mathrm{Ba}}_{14}{\mathrm{MnBi}}_{11},$ show an unusual magnetic behavior, but the large number (104) of atoms in the primitive cell has precluded any previous full electronic structure study. Using an efficient, local-orbital-based method within the local-spin-density approximation to study the electronic structure, we find a gap between a bonding valence-band complex and an antibonding conduction-band continuum. The bonding bands lack one electron per formula unit of being filled, making them low carrier density p-type metals. The hole resides in the ${\mathrm{MnBi}}_{4}$ tetrahedral unit, and partially compensates for the high-spin ${d}^{5} \mathrm{Mn}$ moment, leaving a net spin near $4{\ensuremath{\mu}}_{B}$ that is consistent with experiment. These manganites are composed of two disjoint but interpenetrating ``jungle gym'' networks of spin-$\frac{4}{2}$ ${\mathrm{MnBi}}_{4}^{9\ensuremath{-}}$ units with ferromagnetic interactions within the same network, and weaker couplings between the networks whose sign and magnitude is sensitive to materials parameters. ${\mathrm{Ca}}_{14}{\mathrm{MnBi}}_{11}$ is calculated to be ferromagnetic as observed, while for ${\mathrm{Ba}}_{14}{\mathrm{MnBi}}_{11}$ (which is antiferromagnetic) the ferromagnetic and antiferromagnetic states are calculated to be essentially degenerate. The band structure of the ferromagnetic states is very close to half metallic.