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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). ; Peer reviewed

DOE Early Career Awards ; Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) ; ICTP-Simons Associate Scheme ; FP7 FET-ICT Planar Atomic and Molecular Scale devices (PAMS) project (European Commission) ; Spanish Agencia Estatal de Investigacion ; Dep. de Educacion of the Basque Government ; UPV/EHU ; US Department of Energy ; DOE Early Career Awards: DE-SC0003871 ; DOE Early Career Awards: DE-FG02-09ER16052 ; Processo FAPESP: 2011/11973-4 ; FP7 FET-ICT Planar Atomic and Molecular Scale devices (PAMS) project (European Commission): 610446 ; Spanish Agencia Estatal de Investigacion: MAT2016-78293-C6-4-R ; UPV/EHU: IT-756-13 ; US Department of Energy: DE-AC02-98CH10886 ; Understanding the local structure of water at the interfaces of metallic electrodes is a key issue in aqueousbased electrochemistry. Nevertheless a realistic simulation of such a setup is challenging, particularly when the electrodes are maintained at different potentials. To correctly compute the effect of an external bias potential applied to truly semi-infinite surfaces, we combine Density Functional Theory (DFT) and NonEquilibrium Green's Function (NEGF) methods. This framework allows for the out-of-equilibrium calculation of forces and dynamics, and directly correlates to the chemical potential of the electrodes, which is introduced experimentally. In this work, we apply this methodology to study the electronic properties and atomic forces of a water molecule at the interface of a gold surface. We find that the water molecule tends to align its dipole moment with the electric field, and it is either repelled or attracted to the metal depending on the sign and magnitude of the applied bias, in an asymmetric fashion.

Understanding the local structure of water at the interfaces of metallic electrodes is a key issue in aqueous-based electrochemistry. Nevertheless a realistic simulation of such a setup is challenging, particularly when the electrodes are maintained at different potentials. To correctly compute the effect of an external bias potential applied to truly semi-infinite surfaces, we combine Density Functional Theory (DFT) and Non-Equilibrium Green's Function (NEGF) methods. This framework allows for the out-of-equilibrium calculation of forces and dynamics, and directly correlates to the chemical potential of the electrodes, which is introduced experimentally. In this work, we apply this methodology to study the electronic properties and atomic forces of a water molecule at the interface of a gold surface. We find that the water molecule tends to align its dipole moment with the electric field, and it is either repelled or attracted to the metal depending on the sign and magnitude of the applied bias, in an asymmetric fashion. ; The work was funded by DOE Early Career Awards No. DE-SC0003871 and DE-FG02-09ER16052. L. S. P. and A. R. R. also acknowledge financial support from ICTP-SAIFR (FAPESP project No. 2011/11973-4) and the ICTP-Simons Associate Scheme. P. B. acknowledges financial support from the FP7 FET-ICT "Planar Atomic and Molecular Scale devices" (PAMS) project (funded by the European Commission under contract No. 610446), the Spanish Agencia Estatal de Investigación (Grant No. MAT2016-78293-C6-4-R) and the Dep. de Educación of the Basque Government and UPV/EHU (Grant No. IT-756-13). This research used computational resources at the Center for Functional Nanomaterials, Brookhaven National Laboratory, which is supported by the US Department of Energy under Contract No. DE-AC02-98CH10886 and the S. Dumont supercomputer at the National Laboratory for Scientific Computing (LNCC/MCTI, Brazil). ; Peer Reviewed

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). ; Peer reviewed

Trabajo presentado al Symposium on Surface Science (3S), celebrado en Austria del 1 al 7 de marzo de 2020. ; 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. ; Peer reviewed

Trabajo presentado al Symposium on Surface Science (3S), celebrado en Austria del 1 al 7 de marzo de 2020. ; Support by the European Union FET Open project SPRING (grant 863098) and by the Spanish Ministry of Economy and Competitiveness, MINECO (grants FIS2017-83780-P and MAT2016-78293-C6). ; Peer reviewed

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- ; Peer reviewed

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. ; Peer reviewed

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). ; Peer Reviewed

This document is the unedited Author's version of a Submitted Work that was subsequently accepted for publication in ACS Nano, copyright © American Chemical Society after peer review. To access the final edited and published work see https://doi.org/10.1021/acsnano.0c01837 ; The on-surface synthesis of edge-functionalized graphene nanoribbons (GNRs) is challenged by the stability of the functional groups throughout the thermal reaction steps of the synthetic pathway. Edge fluorination is a particularly critical case in which the interaction with the catalytic substrate and intermediate products can induce the complete cleavage of the otherwise strong C–F bonds before the formation of the GNR. Here, we demonstrate how a rational design of the precursor can stabilize the functional group, enabling the synthesis of edge-fluorinated GNRs. The survival of the functionalization is demonstrated by tracking the structural and chemical transformations occurring at each reaction step with complementary X-ray photoelectron spectroscopy and scanning tunneling microscopy measurements. In contrast to previous attempts, we find that the C–F bond survives the cyclodehydrogenation of the intermediate polymers, leaving a thermal window where GNRs withhold more than 80% of the fluorine atoms. We attribute this enhanced stability of the C–F bond to the particular structure of our precursor, which prevents the cleavage of the C–F bond by avoiding interaction with the residual hydrogen originated in the cyclodehydrogenation. This structural protection of the linking bond could be implemented in the synthesis of other sp2-functionalized GNRs ; C.M. was supported by the Agency for Management of University and Research grants (AGAUR) of the Catalan government through the FP7 framework program of the European Commission under Marie Curie COFUND action 600385 funded by the CERCA Program/Generalitat de Catalunya. We acknowledge support from the Spanish Ministry of Economy and Competitiveness, MINECO (under Contracts Nos. MAT2016-78293-C6 ...

High-quality graphene nanoribbons (GNRs) grown by on-surface synthesis strategies with atomic precision can be controllably doped by inserting heteroatoms or chemical groups in the molecular precursors. Here, we study the electronic structure of armchair GNRs substitutionally doped with di-boron moieties at the center, through a combination of scanning tunneling spectroscopy, angle-resolved photoemission, and density functional theory simulations. Boron atoms appear with a small displacement toward the surface, signaling their stronger interactions with the metal. We find two boron-rich flat bands emerging as impurity states inside the GNR band gap, one of them particularly broadened after its hybridization with the gold surface states. In addition, the boron atoms shift the conduction and valence bands of the pristine GNR away from the gap edge and leave unaffected the bands above and below, which become the new frontier bands and have a negligible boron character. This is due to the selective mixing of boron states with GNR bands according to their symmetry. Our results depict that the GNR band structure can be tuned by modifying the separation between di-boron moieties. ; We acknowledge financial support from the Basque Government (Departamento de Industria, grant no. PI-2015-1-42, and Departamento de Educación and UPV/EHU, grant no. IT-756-13), the Spanish Ministerio de Economía y Competitividad (grant nos. MAT2016-78293-C6, FIS2015-62538-ERC, FIS2017-83780-P), the Maria de Maeztu Units of Excellence Programme (MDM-2016-0618), the European Research Council (grant agreement no. 635919), and the European Regional Development Fund. ; Peer Reviewed

Siesta development was historically supported by different Spanish National Plan projects (Project Nos. MEC-DGES-PB95-0202, MCyT-BFM2000-1312, MEC-BFM2003-03372, FIS2006-12117, FIS2009-12721, FIS2012-37549, FIS2015-64886-P, and RTC-2016-5681-7), the latter one together with Simune Atomistics Ltd. We are thankful for financial support from the Spanish Ministry of Science, Innovation and Universities through Grant No. PGC2018-096955-B. We acknowledge the Severo Ochoa Center of Excellence Program [Grant Nos. SEV-2015-0496 (ICMAB) and SEV-2017-0706 (ICN2)], the GenCat (Grant No. 2017SGR1506), and the European Union MaX Center of Excellence (EU-H2020 Grant No. 824143). P.G.-F. acknowledges support from Ramón y Cajal (Grant No. RyC-2013-12515). J.I.C. acknowledges Grant No. RTI2018-097895-B-C41. R.C. acknowledges the European Union's Horizon 2020 Research and Innovation Program under Marie Skłodoswka-Curie Grant Agreement No. 665919. D.S.P, P.K., and P.B. acknowledge Grant No. MAT2016-78293-C6, FET-Open No. 863098, and UPV-EHU Grant No. IT1246-19. V. W. Yu was supported by a MolSSI Fellowship (U.S. NSF Award No. 1547580), and V.B. and V.W.Y. were supported by the ELSI Development by the NSF (Award No. 1450280). We also acknowledge Honghui Shang and Xinming Qin for giving us access to the honpas code, where a preliminary version of the hybrid functional support described here was implemented. ; García, A., Papior, N., Akhtar, A., Artacho, E., Blum, V., Bosoni, E., Brandimarte, P., Brandbyge, M., Cerdá, J.I., Corsetti, F., Cuadrado, R., Dikan, V., Ferrer, J., Gale, J., García-Fernández, P., García-Suárez, V.M., García, S., Huhs, G., Illera, S., Korytár, R., Koval, P., Lebedeva, I., Lin, L., López-Tarifa, P., Mayo, S.G., Mohr, S., Ordejón, P., Postnikov, A., Pouillon, Y., Pruneda, M., Robles, R., Sánchez-Portal, D., Soler, J.M., Ullah, R., Yu, V.W.-Z., Junquera, J.

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 real-space 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 has been historically supported by different Spanish National Plan projects: MEC-DGESPB95-0202, 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. Currently, we thank financial support from the Spanish Ministry of Science, Innovation and Universities through the grant No. PGC2018-096955-B. We acknowledge the Severo Ochoa Centers of Excellence Program under Grants No. 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 RTI2018-097895-B-C41. R.C. acknowledges to the European Union's Horizon 2020 research and innovation program under the Marie Skłodoswka–Curie grant agreement no. 665919. D.S.P, P.K, and P.B acknowledge MAT2016-78293-C6, FET-Open No. 863098, and UPV-EHU Grant IT1246-19. V. Yu was supported by a MolSSI fellowship (U.S. NSF award 1547580), and the ELSI development (V.B.,V.Yu) by NSF award 1450280. We also acknowledge Honghui Shang and Xinming Qin for giving us access to the HONPAS code, where a preliminary version of the hybrid functionals support described here was implemented. We are indebted to other contributors to the SIESTA project, whose names can be seen in the file in the Docs/Contributors.txt file of the SIESTA distribution, and we thank those, too many to list, contributing fixes, comments, clarifications, and documentation for the code. The data that support the findings of this study are available from the corresponding author upon reasonable request. ; Peer Reviewed ; Postprint (author's final draft)