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  • 1.
    Björk, Jonas
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, Faculty of Science & Engineering.
    Formation mechanisms of covalent nanostructures from density functional theory2016In: Proceedings of International Workshop on On-Surface Synthesis, Cham: Springer, 2016, p. 269-287Conference paper (Refereed)
    Abstract [en]

    In this chapter, it is demonstrated how electronic structure calculations, with focus on density functional theory, can be used to gain insight about on-surface reactions. I first give a brief introduction to how density functional theory can be used to study reactions. The focus is then shifted to two different types of on-surface reactions, highlighting the theoretical work that has been performed to gain detailed atomistic insight into them. First, the state of the art of the theory behind on-surface Ullmann coupling is described. In this reaction, molecular building blocks dehalogenate, which enables them to covalently couple. The most crucial reaction parameters are identified—the diffusion and coupling barriers of surface-supported radicals—and the potential for theory to optimize these is discussed. We then concentrate on the homo-coupling between terminal alkynes, a rudimentarily different process where molecules initially couple before undergoing a dehydrogenation step. The theory of the mechanism behind this coupling strategy is less developed than that of the on-surface Ullmann coupling, where fundamental questions remain to be unraveled. For example, by the subtle change of substrate from Ag to Au, the on-surface alkyne chemistry is completely altered from the homo-coupling to a cyclodehydrogenation reaction for the same molecular building block, of which origin remains unknown. The main objective of the chapter is to give an impression of what kind of information theory can obtain about reaction on surface, as well as to motivate and inspire for future theoretical studies, which will be needed to turn on-surface synthesis into a more predictive discipline.

  • 2.
    Björk, Jonas
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, Faculty of Science & Engineering.
    Reaction mechanisms for on-surface synthesis of covalent nanostructures2016In: Journal of Physics: Condensed Matter, ISSN 0953-8984, E-ISSN 1361-648X, Vol. 28, no 8, p. 083002-Article, review/survey (Refereed)
    Abstract [en]

    In recent years, on-surface synthesis has become an increasingly popular strategy to form covalent nanostructures. The approach has great prospects for facilitating the manufacture of a range of fascinating materials with atomic precision. However, the on-surface reactions are enigmatic to control, currently restricting its bright perspectives and there is a great need to explore how the reactions are governed. The objective of this topical review is to summarize theoretical work that has focused on comprehending on-surface synthesis protocols through studies of reaction mechanisms.

  • 3.
    Björk, Jonas
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Hanke, Felix
    Accelrys, 334 Science Park, Cambridge, CB4 0WN, United Kingdom.
    Towards Design Rules for Covalent Nanostructures on Metal Surfaces2014In: Chemistry - A European Journal, ISSN 0947-6539, E-ISSN 1521-3765, Vol. 20, no 4, p. 928-934Article in journal (Refereed)
    Abstract [en]

    The covalent molecular assembly on metal surfaces is explored, outlining the different types of applicable reactions. Density functional calculations for on-surface reactions are shown to yield valuable insights into specific reaction mechanisms and trends across the periodic table. Finally, it is shown how design rules could be derived for nanostructures on metal surfaces.

  • 4.
    Björk, Jonas
    et al.
    University of Liverpool, UK.
    Hanke, Felix
    University of Liverpool, UK.
    Palma, Carlos-Andres
    University de Strasbourg, France.
    Samorì, Paolo
    University de Strasbourg, France.
    Cecchini, Marco
    University de Strasbourg, France.
    Persson, Mats
    University of Liverpool, UK.
    Adsorption of Aromatic and Anti-Aromatic Systems on Graphene through π−π Stacking2010In: Journal of Physical Chemistry Letters, ISSN 1948-7185, E-ISSN 1948-7185, Vol. 1, p. 3407-3412Article in journal (Refereed)
    Abstract [en]

    The adsorption of neutral (poly)-aromatic, antiaromatic, and more generally π-conjugated systems on graphene is studied as a prototypical case of π-π stacking. To account for dispersive interactions, we compare the recent van der Waals density functional (vdw-DF) with three semiempirical corrections to density functional theory and two empirical force fields. The adsorption energies of the molecules binding to graphene predicted by the vdw-DFwere found to be in excellent agreement with temperature desorption experiments reported in litera- ture,whereas the results of theremaining functionals andforce fields only preserve the correct trends. The comparison of the dispersive versus electrostatic contribu- tions to the total binding energies in the aromatic and antiaromatic systems suggests that π-π interactions can be regarded as being prevalently dispersive in nature at large separations, whereas close to the equilibrium bonding distance, it is a complex interplay between dispersive and electrostatic Coulombic interactions. Moreover our results surprisingly indicate that the magnitude of π-π interactions normalized both per number of total atoms and carbon atoms increases signifi- cantly with the relative number of hydrogen atoms in the studied systems.

  • 5.
    Björk, Jonas
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Hanke, Felix
    Surface Science Research Centre, University of Liverpool, UK.
    Stafström, Sven
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Mechanisms of halogen-based covalent self-assembly on metal surfaces2013In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 135, no 15, p. 5768-5775Article in journal (Refereed)
    Abstract [en]

    We computationally study the reaction mechanisms of halogen-based covalent self-assembly, a major route for synthesizing molecular nanostructures and nanographenes on surfaces. Focusing on biphenyl as a small model system, we describe the dehalogenation, recombination, and diffusion processes. The kinetics of the different processes are also investigated, in particular how diffusion and coupling barriers affect recombination rates. Trends across the periodic table are derived from three commonly used close-packed (111) surfaces (Cu, Ag, and Au) and two halogens (Br and I). We show that the halogen atoms can poison the surface, thus hindering long-range ordering of the self-assembled structures. Finally, we present core-level shifts of the relevant carbon and halogen atoms, to provide reference data for reliably detecting self-assembly without the need for atomic-resolution scanning tunneling microscopy.

  • 6.
    Björk, Jonas
    et al.
    University of Liverpool, UK.
    Matena, Manfred
    University of Basel, Switzerland.
    Dyer, Matthew S.
    University of Liverpool, UK.
    Enache, Mihaela
    University of Basel, Switzerland.
    Lobo-Checa, Jorge
    University of Basel, Switzerland.
    Gade, Lutz H.
    University of Heidelberg, Germany.
    Jung, Thomas A.
    Paul-Scherrer-Institute, Villigen, Switzerland.
    Stöhr, Meike
    University of Basel, Switzerland.
    Persson, Mats
    University of Liverpool, UK.
    STM fingerprint of molecule-adatom interactions in a self-assembled metal-organic surface coordination network on Cu(111)2010In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 12, p. 8815-8821Article in journal (Refereed)
    Abstract [en]

    A novel approach of identifying metal atoms within a metal-organic surface coordination network using scanning tunnelling microscopy (STM) is presented. The Cu adatoms coordinated in the porous surface network of 1,3,8,10-tetraazaperopyrene (TAPP) molecules on a Cu(111) surface give rise to a characteristic electronic resonance in STM experiments. Using density functional theory calculations, we provide strong evidence that this resonance is a fingerprint of the interaction between the molecules and the Cu adatoms. We also show that the bonding of the Cu adatoms to the organic exodentate ligands is characterised by both the mixing of the nitrogen lone-pair orbitals of TAPP with states on the Cu adatoms and the partial filling of the lowest unoccupied molecular orbital (LUMO) of the TAPP molecule. Furthermore, the key interactions determining the surface unit cell of the network are discussed.

  • 7.
    Björk, Jonas
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Stafström, Sven
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Adsorption of large hydrocarbons on coinage metals: a van der Waals density functional study2014In: ChemPhysChem, ISSN 1439-4235, E-ISSN 1439-7641, Vol. 15, no 13, p. 2851-2858Article in journal (Refereed)
    Abstract [en]

    The adsorption of organic molecules onto the close-packed facets of coinage metals is studied, and how accurately adsorption heights can be described by using recent advances of the van der Waals density functional (vdWDF), with optPBE/vdWDF, optB86b/vdWDF, vdWDF2, and rev/vdWDF2 functionals is illustrated. The adsorption of two prototypical aromatic hydrocarbons is investigated, and the calculated adsorption heights are compared to experimental literature values from normal incident X-ray standing wave absorption and a state-of-the-art semi-empirical method. It is shown that both the optB86b/vdWDF and rev/vdWDF2 functionals describe adsorption heights with an accuracy of 0.1 Å, compared to experimental values, and are concluded as reliable methods of choice for related systems.

  • 8.
    Björk, Jonas
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics . Linköping University, The Institute of Technology.
    Stafström, Sven
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics . Linköping University, The Institute of Technology.
    Hanke, Felix
    University of Liverpool.
    Zipping Up: Cooperativity Drives the Synthesis of Graphene Nanoribbons2011In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 133, no 38, p. 14884-14887Article in journal (Refereed)
    Abstract [en]

    We investigate the cooperative effects controlling the synthesis of a graphene nanoribbon on the Au(111) surface starting from an anthracene polymer using density functional calculations including van der Waals interactions. We focus on the high-temperature cyclodehydrogenation step of the reaction and find that the reaction proceeds by simultaneously transferring two H-atoms from the anthracene units to the Au surface, leaving behind a C C bond in the process. This step is significantly more favorable than the three other potential reaction paths. Moreover, we find that successive dehydrogenations proceed from one end of the polyanthracene and propagate step-by-step through the polymer in a domino-like fashion.

  • 9.
    Björk, Jonas
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Zhang, Yi-Qi
    Technische Universität München, Garching, Germany.
    Klappenberger, Florian
    Technische Universität München, Garching, Germany.
    Barth, Johannes V.
    Technische Universität München, Garching, Germany.
    Stafström, Sven
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Unraveling the Mechanism of the Covalent Coupling Between Terminal Alkynes on a Noble Metal2014In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 118, no 6, p. 3181-3187Article in journal (Refereed)
    Abstract [en]

    The mechanism of the newly reported route for surface-assisted covalent coupling of terminal alkynes on Ag(111) is unraveled by density functional theory based transition state calculations. We illustrate that the reaction path is fundamentally different from the classical coupling schemes in wet chemistry. It is initiated by the covalent coupling between two molecules instead of single-molecule dehydrogenation. The silver substrate is found to play an important role stabilizing the intermediate species by chemical bonds, although it is hardly active electronically in the actual coupling step. The dimer intermediate is concluded to undergo two subsequent dehydrogenation processes expected to be rate-limiting according to the comparatively large barriers, which origin is discussed.

  • 10.
    Bronner, Christopher
    et al.
    Heidelberg Univ, Phys Chem Inst, D-69120 Heidelberg, Germany ; Free Univ Berlin, Fachbereich Phys, D-14195 Berlin, Germany.
    Björk, Jonas
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, The Institute of Technology.
    Tegeder, Petra
    Heidelberg Univ, Phys Chem Inst, D-69120 Heidelberg, Germany ; Free Univ Berlin, Fachbereich Phys, D-14195 Berlin, Germany.
    Tracking and removing Br during the on-surface synthesis of a graphene nanoribbon2015In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 119, no 1, p. 486-493Article in journal (Refereed)
    Abstract [en]

    The fabrication of graphene nanoribbons (GNRs) requires a high degree of precision due to the sensitivity of the electronic structure on the edge shape. Using Br-substituted molecular precursors, this atomic precision can be achieved in a thermally induced two-step reaction following Br dissociation on a Au(111) surface. Using DFT, we find evidence that the Br atoms are bound to the intermediate polyanthrylene chains. We employ temperature-programmed desorption to demonstrate the associative desorption of HBr and molecular hydrogen during the final cyclodehydrogenation step of the reaction. Both processes are found to have similar activation barriers. Furthermore, we are able to remove Br atoms from the polyanthrylene chains by providing molecular hydrogen. The subsequent formation of GNR via a cyclodehydrogenation demonstrates that Br does not influence this part of the overall reaction.

  • 11.
    Cirera, Borja
    et al.
    IMDEA Nanoscience, c/Faraday 9, Cantoblanco,Madrid, Spain.
    Giménez-Agulló, Nelson
    Institute of Chemical Research of Catalonia, Barcelona Institute of Science and Technology, Avinguda Pa¨ısos Catalans 16, Tarragona, Spain.
    Björk, Jonas
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, Faculty of Science & Engineering.
    Martínez-Peña, Francisco
    IMDEA Nanoscience, c/Faraday 9, Cantoblanco,Madrid, Spain..
    Martin-Jimenez, Alberto
    IMDEA Nanoscience, c/Faraday 9, Cantoblanco,Madrid, Spain..
    Rodriguez-Fernandez, Jonathan
    Departamento de F´ısica de la Materia Condensada, Universidad Auto´noma de Madrid, c/Francisco Toma´s y Valiente.
    Pizarro, Ana M.
    IMDEA Nanoscience, c/Faraday 9, Cantoblanco,Madrid, Spain..
    Otero, Roberto
    IMDEA Nanoscience, c/Faraday 9, Cantoblanco, 28049 Madrid, Spain,Universidad Auto´noma de Madrid, c/Francisco Toma´s y Valiente.
    Gallego, José M.
    Instituto de Ciencia de Materiales de Madrid, c/ Sor Juana Ine´s de la Cruz 3, Cantoblanco,Madrid, Spain..
    Ballester, Pablo
    Institute of Chemical Research of Catalonia, Barcelona Institute of Science and Technology, Avinguda Pa¨ısos Catalans 16, Tarragona, Spain/Catalan Institutionfor Research and Advanced Studies, Passeig Lluis Companys 23, Barcelona, Spain..
    Galan-Mascaros, José R.
    Institute of Chemical Research of Catalonia, Barcelona Institute of Science and Technology, Avinguda Pa¨ısos Catalans 16, Tarragona, Spain/Catalan Institutionfor Research and Advanced Studies, Passeig Lluis Companys 23, Barcelona, Spain..
    Ecija, David
    IMDEA Nanoscience, c/Faraday 9, Cantoblanco, Madrid, Spain.
    Thermal selectivity of intermolecular versus intramolecular reactions on surfaces2016In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 7, no 11002Article in journal (Refereed)
    Abstract [en]

    On-surface synthesis is a promising strategy for engineering heteroatomic covalent nanoarchitectures with prospects in electronics, optoelectronics and photovoltaics. Here we report the thermal tunability of reaction pathways of a molecular precursor in order to select intramolecular versus intermolecular reactions, yielding monomeric or polymeric phthalocyanine derivatives, respectively. Deposition of tetra-aza-porphyrin species bearing ethyl termini on Au(111) held at room temperature results in a close-packed assembly. Upon annealing from room temperature to 275 °C, the molecular precursors undergo a series of covalent reactions via their ethyl termini, giving rise to phthalocyanine tapes. However, deposition of the tetra-aza-porphyrin derivatives on Au(111) held at 300 °C results in the formation and self-assembly of monomeric phthalocyanines. A systematic scanning tunnelling microscopy study of reaction intermediates, combined with density functional calculations, suggests a [2+2] cycloaddition as responsible for the initial linkage between molecular precursors, whereas the monomeric reaction is rationalized as an electrocyclic ring closure.

  • 12.
    Gottardi, Stefano
    et al.
    University of Groningen, Netherlands.
    Muller, Kathrin
    University of Groningen, Netherlands.
    Bignardi, Luca
    University of Groningen, Netherlands.
    Carlos Moreno-Lopez, Juan
    University of Groningen, Netherlands.
    Tuan Anh Pham; Ivashenko, Oleksii
    University of Groningen, Netherlands.
    Yablonskikh, Mikhail
    Sincrotrone Trieste Scpa, Italy.
    Barinov, Alexei
    Sincrotrone Trieste Scpa, Italy.
    Björk, Jonas
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, The Institute of Technology.
    Rudolf, Petra
    University of Groningen, Netherlands.
    Stohr, Meike
    University of Groningen, Netherlands.
    Comparing Graphene Growth on Cu(111) versus Oxidized Cu(111)2015In: Nano letters (Print), ISSN 1530-6984, E-ISSN 1530-6992, Vol. 15, no 2, p. 917-922Article in journal (Refereed)
    Abstract [en]

    The epitaxial growth of graphene on catalytically active metallic surfaces via chemical vapor deposition (CVD) is known to be one of the most reliable routes toward high-quality large-area graphene. This CVD-grown graphene is generally coupled to its metallic support resulting in a modification of its intrinsic properties. Growth on oxides is a promising alternative that might lead to a decoupled graphene layer. Here, we compare graphene on a pure metallic to graphene on an oxidized copper surface in both cases grown by a single step CVD process under similar conditions. Remarkably, the growth on copper oxide, a high-k dielectric material, preserves the intrinsic properties of graphene; it is not doped and a linear dispersion is observed close to the Fermi energy. Density functional theory calculations give additional insight into the reaction processes and help explaining the catalytic activity of the copper oxide surface.

  • 13.
    Hanke, Felix
    et al.
    Surface Science Research Centre, University of Liverpool, UK.
    Björk, Jonas
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Structure and local reactivity of the Au(111) surface reconstruction2013In: Physical Review B. Condensed Matter and Materials Physics, ISSN 1098-0121, E-ISSN 1550-235X, Vol. 87, no 23Article in journal (Refereed)
    Abstract [en]

    The close-packed (111) surface of gold is well known to show a 22×√3 reconstruction on single nm lengths with a long-range herringbone pattern on scales of a few hundred nm. Here we investigate the local reconstruction using density functional theory and compare the results to scanning tunneling microscopy experiments. Moreover, we use hydrogen and fluorine as probe atoms to investigate changes in the ability of the Au(111) surface to catalyze the reactions involved in the formation of molecular nanostructures. We find a small variation of the reactivity across different surface sites and link those results to the local coordination environment of the face-centered-cubic (fcc), hexagonal-close-packed (hcp), and ridge regions. Finally, we scrutinize a commonly used approximation in density functional studies, namely that Au(111) is atomically flat and a perfect termination of the fcc lattice.

  • 14.
    Hanke, Felix
    et al.
    Surface Science Research Centre, University of Liverpool, UK.
    Dyer, Matthew S.
    Surface Science Research Centre, University of Liverpool, UK.
    Björk, Jonas
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Persson, Mats
    Surface Science Research Centre, University of Liverpool, UK.
    Structure and stability of weakly chemisorbed ethene adsorbed on low-index Cu surfaces: performance of density functionals with van der Waals interactions2012In: Journal of Physics: Condensed Matter, ISSN 0953-8984, E-ISSN 1361-648X, Vol. 42, p. 424217-424225Article in journal (Refereed)
    Abstract [en]

    We have investigated the performance of popular density functionals that include van der Waals interactions for the experimentally well-characterized problem of ethene (C(2)H(4)) adsorbed on the low-index surfaces of copper. This set of functionals does not only include three van der Waals density functionals-vdwDF-PBE, vdwDF-revPBE and optB86b-vdwDF-and two dispersion-corrected functionals-Grimme and TS-but also local and semi-local functionals such as LDA and PBE. The adsorption system of ethene on copper was chosen because it is a weakly chemisorbed system for which the vdW interactions are expected to give a significant contribution to the adsorption energy. Overall the density functionals that include vdW interactions increased substantially the adsorption energies compared to the PBE density functional but predicted the same adsorption sites and very similar C-C bonding distances except for two of the van der Waals functionals. The top adsorption site was predicted almost exclusively for all functionals on the (110), (100) and (111) surfaces, which is in agreement with experiment for the (110) surface but not for the (100) surface. On the (100) surface, all functionals except two van der Waals density functionals singled out the observed cross-hollow site from the calculated C-C bonding distances and adsorption heights. On the top sites on the (110) surface and the cross-hollow site on the Cu(100) surface, the ethene molecule was found to form a weak chemisorption bond. On the (111) surface, all functionals gave a C-C bonding distance and an adsorption height more typical for physisorption, in agreement with experiments.

  • 15.
    Honkela, Maija
    et al.
    Aalto University, Finland.
    Björk, Jonas
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Persson, Mats
    Surface Science Research Centre, University of Liverpool, UK.
    Computational study of the adsorption and dissociation of phenol on Pt and Rh surfaces2012In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 14, no 16, p. 5849-5854Article in journal (Refereed)
    Abstract [en]

    The adsorption of phenol on flat and stepped Pt and Rh surfaces and the dissociation of hydrogen from the hydroxyl group of phenol on Pt(111) and Rh(111) were studied by density functional calculations. On both Pt(111) and Rh(111), phenol adsorbs with the aromatic ring parallel to the surface and the hydroxyl group tilted away from the surface. Furthermore, adsorption on stepped surfaces was concluded to be unfavourable compared to the (111) surfaces due to the repulsion of the hydroxyl group from the step edges. Transition state calculations revealed that the reaction barriers, associated with the dissociation of phenol into phenoxy, are almost identical on Pt and Rh. Furthermore, the oxygen in the dissociated phenol is strongly attracted by Rh(111), while it is repelled by Pt(111).

  • 16.
    Kawai, Shigeki
    et al.
    Namiki, Tsukuba, 305-0044 Ibaraki, Japan/Basel, Switzerland/ Honcho, Kawaguchi, 332-0012 Saitama, Japan.
    Foster, Adam S.
    Aalto University, Finland/Kanazawa University, Kanazawa Japan..
    Björkman, Torbjörn
    Aalto University/Åbo Akademi University, Finland..
    Nowakowska, Sylwia
    University of Basel,Switzerland.
    Björk, Jonas
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, Faculty of Science & Engineering.
    Canova, Filippo Federici
    Aalto University, Finland.
    Gade, Lutz H.
    Universität Heidelberg, Germany.
    Jung, Thomas A.
    University of Basel, Switzerland/Paul Scherrer Institute, Switzerland..
    Meyer, Ernst
    University of Basel, Switzerland..
    Van der Waals interactions and the limits of isolated atom models at interfaces2016In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 7, article id 11559Article in journal (Refereed)
    Abstract [en]

    Van der Waals forces are among the weakest, yet most decisive interactions governing condensation and aggregation processes and the phase behaviour of atomic and molecular matter. Understanding the resulting structural motifs and patterns has become increasingly important in studies of the nanoscale regime. Here we measure the paradigmatic van der Waals interactions represented by the noble gas atom pairs Ar–Xe, Kr–Xe and Xe–Xe with a Xe-functionalized tip of an atomic force microscope at low temperature. Individual rare gas atoms were fixed at node sites of a surface-confined two-dimensional metal–organic framework. We found that the magnitude of the measured force increased with the atomic radius, yet detailed simulation by density functional theory revealed that the adsorption induced charge redistribution strengthened the van der Waals forces by a factor of up to two, thus demonstrating the limits of a purely atomic description of the interaction in these representative systems.

  • 17.
    Kepčija, Nenad
    et al.
    Technische Universität München, Germany.
    Zhang, Yi-Qi
    Technische Universität München, Germany.
    Kleinschrodt, Martin
    Technische Universität München, Germany.
    Björk, Jonas
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Klyatskaya, Svetlana
    Karlsruhe Institute of Technology, Germany.
    Klappenberger, Florian
    Technische Universität München, Germany.
    Ruben, Mario
    Karlsruhe Institute of Technology, Germany.
    Barth, Johannes V.
    Technische Universität München, Germany.
    Steering On-Surface Self-Assembly of High-Quality Hydrocarbon Networks with Terminal Alkynes2013In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 117, no 8, p. 3987-3995Article in journal (Refereed)
    Abstract [en]

    The two-dimensional (2D) self-assembly of 1,3,5-triethynyl-benzene (TEB) and de novo synthesized 1,3,5-tris-(4-ethynylphenyl)benzene (Ext-TEB) on Ag(111) was investigated by means of scanning tunneling microscopy (STM) under ultrahigh vacuum (UHV) conditions. Both 3-fold symmetric molecules form long-range ordered nanoporous networks featuring organizational chirality, mediated by novel, planar 6-fold cyclic binding motifs. The key interaction for the expression of the motifs is identified as C–H···π bonding. For Ext-TEB, an additional open-porous phase exists with the 3-fold motif. The nature of the underlying noncovalent bonding schemes is thoroughly analyzed by density functional theory (DFT) calculations including van der Waals corrections. The comparison of calculations focusing on isolated 2D molecular sheets and those including the substrate reveals the delicate balance between the attractive molecule–molecule interaction, mediated by both the terminal alkyne and the phenyl groups, and the molecule–substrate interaction responsible for the commensurability and the regularity of the networks. Comparison with bulk structures of similar molecules suggests that these strictly planar cyclic binding motifs appear only in 2D environments.

  • 18.
    Klappenberger, Florian
    et al.
    Technical University of Munich, Germany.
    Zhang, Yi-Qi
    Technical University of Munich, Germany.
    Björk, Jonas
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, Faculty of Science & Engineering.
    Klyatskaya, Svetlana
    Karlsruhe Institute Technology, Germany.
    Ruben, Mario
    Karlsruhe Institute Technology, Germany; University of Strasbourg, France.
    Barth, Johannes V.
    Technical University of Munich, Germany.
    On-Surface Synthesis of Carbon-Based Scaffolds and Nanomaterials Using Terminal Alkynes2015In: Accounts of Chemical Research, ISSN 0001-4842, E-ISSN 1520-4898, Vol. 48, no 7, p. 2140-2150Article, review/survey (Refereed)
    Abstract [en]

    CONSPECTUS: The covalent linking of acetylene compounds is an important synthetic tool to control carbon carbon bond formation and has been extensively studied for more than a century. Notably, Glaser coupling and subsequently developed refined procedures present an important route for the fabrication of distinct carbon-based scaffolds incorporating units with both sp(2)- and sp-hybridizations, such as carbyne chains, or two-dimensional (2D) graphyne or graphdiyne networks. However, the realization of the envisioned regular low-dimensional compounds and nanoarchitectures poses formidable challenges when following conventional synthesis protocols in solution, which we briefly overview. Now, recent developments in on-surface synthesis establish novel means for the construction of tailored covalent nanostructures under ultrahigh vacuum conditions. Here we focus on the exploration of pathways utilizing interfacial synthesis with terminal alkynes toward the atomically precise fabrication of low-dimensional carbon-rich scaffolds and nanomaterials. We review direct, molecular-level investigations, mainly relying on scanning probe microscopy, providing atomistic insights into thermally activated reaction schemes, their special pathways and products. Using custom-made molecular units, the employed homocoupling, cyclotrimerization, cycloaddition, and radical cyclization processes indeed yield distinct compounds, extended oligomers or 2D networks. Detailed insights into surface interactions such as bonding sites or conformational adaptation, and specific reaction mechanisms, including hierarchic pathways, were gained by sophisticated density functional theory calculations, complemented by X-ray spectroscopy measurements. For the fabrication of regular nanostructures and architectures, it is moreover imperative to cope with spurious side reactions, frequently resulting in chemical diversity. Accordingly, we highlight measures for increasing chemo- and regioselectivity by smart precursor design, substrate templating, and external stimuli. The ensuing preorganization of functional groups and control of side reactions increases product yields markedly. Finally, the electronic band structures of selected cases of novel low-dimensional hydrocarbon materials accessible with the monomers employed to date are discussed with a specific focus on their differences to theoretically established graphyne- and graphdiyne-related scaffolds. The presented methodology and gained insights herald further advancements in the field, heading toward novel molecular compounds, low-dimensional nanostructures, and coherently reticulated polymeric layers, eventually presenting well-defined arrangements with specific carbon carbon bond sequencing and electronic characteristics. The functional properties of these or other foreseeable scaffolds and architectures bear significant prospects for a wide range of applications, for example, in nanoelectronics, photonics, or carbon-based technologies.

  • 19.
    Matena, Manfred
    et al.
    Department of Physics, University of Basel, Basel, Switzerland, Donostia International Physics Center, San Sebastian, Spain .
    Björk, Jonas
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology. Surface Science Research Centre, Department of Chemistry, University of Liverpool, Liverpool, United Kingdom.
    Wahl, Markus
    Department of Physics, University of Basel, Basel, Switzerland.
    Lee, Tien-Lin
    European Synchrotron Radiation Facility, Grenoble, France.
    Zegenhagen, Jörg
    European Synchrotron Radiation Facility, Grenoble, France.
    Gade, Lutz H.
    Anorganisch-Chemisches Institut, Universität Heidelberg, Heidelberg, Germany.
    Jung, Thomas A.
    Department of Physics, University of Basel, Basel, Switzerland, Laboratory for Micro- and Nanotechnology, Villigen, Switzerland.
    Persson, Mats
    Surface Science Research Centre, University of Liverpool, UK, Department of Applied Physics, Chalmers University of Technology, Gothenburg, Sweden.
    Stöhr, Meike
    Department of Physics, University of Basel, Basel, Switzerland, Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands.
    On-surface synthesis of a two-dimensional porous coordination network: Unraveling adsorbate interactions2014In: Physical Review B. Condensed Matter and Materials Physics, ISSN 1098-0121, E-ISSN 1550-235X, Vol. 90, p. 125408-125415Article in journal (Refereed)
    Abstract [en]

    We present a detailed experimental and theoretical characterization of the adsorption of the perylene derivative 4,9-diaminoperylene-quinone-3,10-diimine (DPDI) on Cu(111) and compare it to its threefold dehydrogenated derivative 3deh-DPDI, which forms in a surface reaction upon annealing. While DPDI itself does not give rise to long-range ordered structures due to lack of appropriate functional groups, 3deh-DPDI acts as an exoligand in a Cu-coordinated honeycomb network on Cu(111). The main focus of this work lies on the analysis of intermolecular and molecule-substrate interactions by combining results from scanning tunneling microscopy, x-ray photoelectron spectroscopy, x-ray standing wave measurements, and density functional theory. We show, in particular, that the interactions between metal atoms and organic ligands effectively weaken the molecule-surface interactions for 3deh-DPDI leading to an increase in molecule-substrate distances compared to the DPDI precursor. Our experimental findings also shed light on the applicability of current theories, namely van der Waals corrections to density functional theory.

  • 20.
    Matena, Manfred
    et al.
    University of Basel, Switzerland.
    Stöhr, Meike
    University of Basel, Switzerland.
    Riehm, Till
    University of Heidelberg, Germany.
    Björk, Jonas
    University of Liverpool, UK.
    Martens, Susanne
    University of Heidelberg, Germany.
    Dyer, Matthew S.
    University of Liverpool, UK.
    Persson, Mats
    University of Liverpool, UK.
    Lobo-Checa, Jorge
    University of Basel, Switzerland.
    Müller, Kathrin
    Paul-Scherrer-Institute, Villigen, Switzerland.
    Enache, Mihaela
    University of Basel, Switzerland.
    Wadepohl, Hubert
    University of Heidelberg, Germany.
    Zegenhagen, Jörg
    European Synchrotron Radiation Facility, Grenoble, France.
    Jung, Thomas A.
    Paul-Scherrer-Institute, Villigen, Switzerland.
    Gade, Lutz H.
    University of Heidelberg, Germany.
    Aggregation and contingent metal/surface reactivity of 1,3,8,10-tetraazaperopyrene (TAPP) on Cu(111)2010In: Chemistry - A European Journal, ISSN 0947-6539, E-ISSN 1521-3765, Vol. 16, no 7, p. 2079-2091Article in journal (Refereed)
    Abstract [en]

    The structural chemistry and reactivity of 1,3,8,10-tetraazaperopyrene (TAPP) on Cu(111) under ultra-high-vacuum (UHV) conditions has been studied by a combination of experimental techniques (scanning tunneling microscopy (STM) and X-ray photoelectron spectroscopy, XPS) and DFT calculations. Depending on the deposition conditions, TAPP forms three main assemblies, which result from initial submonolayer coverages based on different intermolecular interactions: a close-packed assembly similar to a projection of the bulk structure of TAPP, in which the molecules interact mainly through van der Waals (vDW) forces and weak hydrogen bonds; a porous copper surface coordination network; and covalently linked molecular chains. The Cu substrate is of crucial importance in determining the structures of the aggregates and available reaction channels on the surface, both in the formation of the porous network for which it provides the Cu atoms for surface metal coordination and in the covalent coupling of the TAPP molecules at elevated temperature. Apart from their role in the kinetics of surface transformations, the available metal adatoms may also profoundly influence the thermodynamics of transformations by coordination to the reaction product, as shown in this work for the case of the Cu-decorated covalent poly(TAPP-Cu) chains.

  • 21.
    Medeiros, Paulo V. C.
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, The Institute of Technology.
    Müller, Kathrin
    Zernike Institute for Advanced Materials, University of Groningen, The Netherlands.
    Jung, Thomas A.
    Laboratory for Micro- and Nanotechnology, Paul-Scherrer-Institute, Switzerland.
    Gade, Lutz H.
    Anorganisch-Chemisches Institut, Universität Heidelberg, Germany.
    Stafström, Sven
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, The Institute of Technology.
    Björk, Jonas
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, The Institute of Technology.
    Stöhr, Meike
    Zernike Institute for Advanced Materials, University of Groningen, The Netherlands.
    Self-assembly of a DPDI+PTCDA mixed layer on Ag(111): Theory and experimentsManuscript (preprint) (Other academic)
    Abstract [en]

    We present a combined experimental and theoretical investigation of the self-assembly of a binary mixture of 4,9-diaminoperylene-quinone-3,10-diimine (DPDI) and 3,4,9,10-perylene-tetracarboxylic acid dianhydride (PTCDA) molecules on Ag(111). At a 1:1 ratio, the two molecules intermix to form a long-range ordered bimolecular network stabilized by intermolecular hydrogen bonding. We show, by means of low energy electron diffraction (LEED) measurements, that the self-assembled network is commensurate with the underlying silver surface. Scanning tunneling microscope (STM) measurements and density functional theory (DFT) calculations are combined to unravel the structural configuration of the system. Core-level binding energy shifts for the 1s levels of the O atoms, obtained from both X-ray photoelectron spectroscopy (XPS) measurements and DFT simulations, are reported and compared. Our DFT calculations allow the investigation of the interplay between molecule-molecule and molecule-surface interactions in the network. Our combined experimental-theoretical approach allows a precise characterization of the structural and electronic properties of the studied system.

  • 22.
    Medeiros, Paulo V. C.
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Stafström, Sven
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Björk, Jonas
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Effects of extrinsic and intrinsic perturbations on the electronic structure of graphene: Retaining an effective primitive cell band structure by band unfolding2014In: Physical Review B. Condensed Matter and Materials Physics, ISSN 1098-0121, E-ISSN 1550-235X, Vol. 89, no 4, p. 041407-1-041407-4Article in journal (Refereed)
    Abstract [en]

    We use a band unfolding technique to recover an effective primitive cell picture of the band structure of graphene under the influence of different types of perturbations. This involves intrinsic perturbations, such as structural defects, and external ones, comprising nitrogen substitutions and the inclusion of graphene in adsorbed systems. In such cases, the band unfolding provides a reliable and efficient tool for quantitatively analyzing the effect of doping and defects on the electronic structure of graphene. We envision that this approach will become a standard method in the computational analysis of graphene's electronic structure in related systems.

  • 23.
    Medeiros, Paulo Vinicius Da Costa
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, The Institute of Technology.
    Tsirpin, Stepan S.
    DIPC, San Sebastian 20018, Basque Country, Spain; Tomsk State Univ, Tomsk 634050, Russia; St Petersburg State Univ, St Petersburg 198504, Russia .
    Stafström, Sven
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, The Institute of Technology.
    Björk, Jonas
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, The Institute of Technology.
    Unfolding spinor wave functions and expectation values of general operators: Introducing the unfolding-density operator2015In: Physical Review B. Condensed Matter and Materials Physics, ISSN 1098-0121, E-ISSN 1550-235X, Vol. 91, p. 041116(R)-041120(R)Article in journal (Refereed)
    Abstract [en]

    We show that the spectral weights W mK ⃗ (k ⃗ ) used for the unfolding of two-component spinor eigenstates ∣ ∣ ψ SC mK ⃗ ⟩=|α⟩|ψ SC mK ⃗ ,α⟩+|β⟩|ψ SC mK ⃗ ,β⟩ can be decomposed as the sum of the partial spectral weights W μ mK ⃗ (k ⃗ ) calculated for each component μ=α,β independently, effortlessly turning a possibly complicated problem involving two coupled quantities into two independent problems of easy solution. Furthermore, we define the unfolding-density operator ρ ˆ K ⃗ (k ⃗ ;ɛ) , which unfolds the primitive cell expectation values φ pc (k ⃗ ;ɛ) of any arbitrary operator φ ˆ according to φ pc (k ⃗ ;ɛ)=Tr(ρ ˆ K ⃗ (k ⃗ ;ɛ)φ ˆ ) . As a proof of concept, we apply the method to obtain the unfolded band structures, as well as the expectation values of the Pauli spin matrices, for prototypical physical systems described by two-component spinor eigenfunctions.

  • 24.
    Morchutt, Claudius
    et al.
    Max Planck Inst Solid State Res, D-70569 Stuttgart, Germany Ecole Polytech Fed Lausanne, Inst Phys Mat Condensee, CH-1015 Lausanne, Switzerland.
    Björk, Jonas
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, The Institute of Technology.
    Krotzky, Sören
    Max Planck Inst Solid State Res, D-70569 Stuttgart, Germany.
    Gutzler, Rico
    Max Planck Inst Solid State Res, D-70569 Stuttgart, Germany.
    Kern, Klaus
    Max Planck Inst Solid State Res, D-70569 Stuttgart, Germany Ecole Polytech Fed Lausanne, Inst Phys Mat Condensee, CH-1015 Lausanne, Switzerland.
    Covalent coupling via dehalogenation on Ni(111) supported boron nitride and graphene2015In: Chemical Communications, ISSN 1359-7345, E-ISSN 1364-548X, Vol. 51, no 12, p. 2440-2443Article in journal (Refereed)
    Abstract [en]

    Polymerization of 1,3,5-tris(4-bromophenyl)benzene via dehalogenation on graphene and hexagonal boron nitride is investigated by scanning tunneling microscopy experiments and density functional theory calculations. This work reveals how the interactions between molecules and graphene or h-BN grown on Ni(111) govern the surface-confined synthesis of polymers through C–C coupling.

  • 25.
    Nowakowska, Sylwia
    et al.
    Univ Basel, Dept Phys, CH-4056 Basel, Switzerland.
    Wäckerlin, Aneliia
    Univ Basel, Dept Phys, CH-4056 Basel, Switzerland.
    Kawai, Shigeki
    Univ Basel, Dept Phys, CH-4056 Basel, Switzerland; Japan Sci & Technol Agcy JST, PRESTO, Kawaguchi, Saitama 3320012, Japan.
    Ivas, Toni
    Univ Basel, Dept Phys, CH-4056 Basel, Switzerland.
    Nowakowski, Jan
    Paul Scherrer Inst, Lab Micro & Nanotechnol, CH-5232 Villigen, Switzerland.
    Fatayer, Shadi
    Univ Basel, Dept Phys, CH-4056 Basel, Switzerland; Univ Estadual Campinas, Inst Fis Gleb Wataghin, Dept Fis Aplicada, BR-13083859 Campinas, Brazil.
    Wäckerlin, Christian
    Paul Scherrer Inst, Lab Micro & Nanotechnol, CH-5232 Villigen, Switzerland.
    Nijs, Thomas
    Univ Basel, Dept Phys, CH-4056 Basel, Switzerland.
    Meyer, Ernst
    Univ Basel, Dept Phys, CH-4056 Basel, Switzerland.
    Björk, Jonas
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, The Institute of Technology.
    Stöhr, Meike
    Univ Groningen, Zernike Inst Adv Mat, NL-9747 AG Groningen, Netherlands.
    Gade, Lutz H.
    Heidelberg Univ, Inst Anorgan Chem, D-69120 Heidelberg, Germany.
    Jung, Thomas A.
    Paul Scherrer Inst, Lab Micro & Nanotechnol, CH-5232 Villigen, Switzerland.
    Interplay of weak interactions in the atom-by-atom condensation of xenon within quantum boxes2015In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 21, no 6, p. 6071-Article in journal (Refereed)
    Abstract [en]

    Condensation processes are of key importance in nature and play a fundamental role in chemistry and physics. Owing to size effects at the nanoscale, it is conceptually desired to experimentally probe the dependence of condensate structure on the number of constituents one by one. Here we present an approach to study a condensation process atom-by-atom with the scanning tunnelling microscope, which provides a direct real-space access with atomic precision to the aggregates formed in atomically defined 'quantum boxes'. Our analysis reveals the subtle interplay of competing directional and nondirectional interactions in the emergence of structure and provides unprecedented input for the structural comparison with quantum mechanical models. This approach focuses on-but is not limited to-the model case of xenon condensation and goes significantly beyond the well-established statistical size analysis of clusters in atomic or molecular beams by mass spectrometry.

  • 26.
    Palma, Carlos-Andres
    et al.
    University of Strasbourg, France.
    Björk, Jonas
    University of Liverpool, UK.
    Bonini, Massimo
    BASF SE..
    Dyer, Matthew S.
    University of Liverpool, UK.
    Llanas-Pallas, Anna
    University of Trieste, Italy.
    Bonifazi, Davide
    University of Trieste, Italy.
    Persson, Mats
    University of Liverpool, UK.
    Samorì, Paolo
    University of Strasbourg, France.
    Tailoring Bicomponent Supramolecular Nanoporous Networks: Phase Segregation, Polymorphism, and Glasses at the Solid−Liquid Interface2009In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 131, no 36, p. 13062-13071Article in journal (Refereed)
    Abstract [en]

    We study the formation of four supramolecular bicomponent networks based on four linear modules (linkers) bridging melamine via triple hydrogen-bonds. We explore at the nanoscale level the phenomena of polymorphism and phase segregation which rule the generation of highly crystalline nanoporous patterns self-assembled at the solid-liquid interface. The investigated linkers include two systems exposing diuracil groups in the R and ω position, naphthalene tetracarboxylic diimide and pyromellitic diimide. In situ scanning tunneling microscopy (STM) investigations revealed that, when blended with melamine, out of the four systems, three are able to form two-dimensional (2D) porous architectures, two of which exhibit highly ordered hexagonal structures, while pyromellitic diimide assembles only into one- dimensional (1D) supramolecular arrays. These bicomponent self-assembled monolayers are used as a test bed to gain detailed insight into phase segregation and polymorphism in 2D supramolecular systems by exploring the contribution of hydrogen-bond energy and periodicity, molecular flexibility, concentration and ratio of the components in solution as well as the effect of annealing via time-dependent and temperature-modulated experiments. These comparative studies, obtained through a joint experimental and computational analysis, offer new insights into strategies toward the bottom-up fabrication of highly ordered tunable nanopatterning at interfaces mediated by hydrogen bonds.

  • 27.
    Palma, Carlos-Andres
    et al.
    Technishe Universität München, Germany.
    Björk, Jonas
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, The Institute of Technology.
    Klappenberger, Florian
    Technische Universität München, Germany.
    Arras, Emmanuel
    Technische Universität München, Germany.
    Kühne, Dirk
    Technische Universität München, Germany.
    Stafström, Sven
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, The Institute of Technology.
    Barth, Johannes V.
    Technische Universität München, Germany.
    Visualization and thermodynamic encoding of single-molecule partition function projections2015In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 6, no 6210Article in journal (Refereed)
    Abstract [en]

    Ensemble averaging of molecular states is fundamental for the experimental determination of thermodynamic quantities. A special case occurs for single-molecule investigations under equilibrium conditions, for which free energy, entropy and enthalpy at finite temperatures are challenging to determine with ensemble averaging alone. Here we report a method to directly record time-averaged equilibrium probability distributions by confining an individual molecule to a nanoscopic pore of a two-dimensional metal-organic nanomesh, using temperature-controlled scanning tunnelling microscopy. We associate these distributions with partition function projections to assess real-space-projected thermodynamic quantities, aided by computational modelling. The presented molecular dynamics-based analysis is able to reproduce experimentally observed projected microstates with high accuracy. By an in silico customized energy landscape, we demonstrate that distinct probability distributions can be encrypted at different temperatures. Such modulation provides means to encode and decode information into position–temperature space.

  • 28.
    Palma, Carlos-Andres
    et al.
    Technishe Universität München, Germany.
    Björk, Jonas
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Rao, Francesco
    Albert-Ludwigs-Universität, Freiburg, Germany.
    Kühne, Dirk
    Technishe Universität München, Germany.
    Klappenberger, Florian
    Technishe Universität München, Germany.
    Barth, Johannes V.
    Technishe Universität München, Germany.
    Topological Dynamics in Supramolecular Rotors2014In: Nano letters (Print), ISSN 1530-6984, E-ISSN 1530-6992, Vol. 14, no 8, p. 4461-4468Article in journal (Refereed)
    Abstract [en]

    Artificial molecular switches, rotors, and machines are set to establish design rules and applications beyond their biological counterparts. Herein we exemplify the role of noncovalent interactions and transient rearrangements in the complex behavior of supramolecular rotors caged in a 2D metal–organic coordination network. Combined scanning tunneling microscopy experiments and molecular dynamics modeling of a supramolecular rotor with respective rotation rates matching with 0.2 kcal mol–1 (9 meV) precision, identify key steps in collective rotation events and reconfigurations. We notably reveal that stereoisomerization of the chiral trimeric units entails topological isomerization whereas rotation occurs in a topology conserving, two-step asynchronous process. In supramolecular constructs, distinct displacements of subunits occur inducing a markedly lower rotation barrier as compared to synchronous mechanisms of rigid rotors. Moreover, the chemical environment can be instructed to control the system dynamics. Our observations allow for a definition of mechanical cooperativity based on a significant reduction of free energy barriers in supramolecules compared to rigid molecules.

  • 29.
    Palma, Carlos-Andres
    et al.
    Technishe Universität München, Garching, Germany.
    Diller, Katharina
    Technishe Universität München, Garching, Germany.
    Berger, Reinhard
    Max-Planck-Institut für Polymerforschung, Mainz, Germany.
    Welle, Alexander
    Karlsruher Institut für Technologie, Eggenstein-Leopoldshafen, Germany.
    Björk, Jonas
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Cabellos, Jose Luis Cabellos
    Universidad del País Vasco UPV/EHU, San Sebastián, Spain.
    Mowbray, Duncan John
    Universidad del País Vasco UPV/EHU, San Sebastián, Spain.
    Papageorgiou, Anthoula C.
    Technishe Universität München, Garching, Germany.
    Ivleva, Natalia P.
    Technische Universität München, München, Germany.
    Matich, Sonja
    Walter Schottky Institut, Garching, Germany.
    Margapoti, Emanuela
    Walter Schottky Institut, Garching, Germany.
    Niesser, Reinhard
    Technische Universität München, Germany.
    Menges, Bernhard
    Max-Planck-Institut für Polymerforschung, Mainz, Germany.
    Reichert, Joachim
    Technishe Universität München, Garching, Germany.
    Feng, Xinliang
    Max-Planck-Institut für Polymerforschung, Mainz, Germany.
    Räder, Hans Joachim
    Max-Planck-Institut für Polymerforschung, Mainz, Germany.
    Klappenberger, Florian
    Technishe Universität München, Garching, Germany.
    Rubio, Angel
    Universidad del País Vasco UPV/EHU, San Sebastián, Spain.
    Müllen, Klaus
    Max-Planck-Institut für Polymerforschung, Mainz, Germany.
    Barth, Johannes V.
    Technishe Universität München, Garching, Germany.
    Photo-induced C-C reactions on insulators towards photolithography of graphene nanoarchitectures2014In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 136, p. 4651-4658Article in journal (Refereed)
    Abstract [en]

    On-surface chemistry for atomically precise sp2 macromolecules requires top-down lithographic methods on insulating surfaces in order to pattern the long-range complex architectures needed by the semiconductor industry. Here, we fabricate sp2-carbon nm-thin films on insulators and under ultra-high vacuum (UHV) conditions from photo-coupled brominated precursors. We reveal that covalent coupling is initiated by C-Br bond cleavage through photon energies exceeding 4.4 eV, as monitored by laser desorption ionization (LDI) mass spectrometry (MS) and X-ray photoelectron spectroscopy (XPS). Density functional theory (DFT) gives insight into the mechanisms of C-Br scission and C-C coupling processes. Further, unreacted material can be sublimed and the coupled sp2-carbon precursors can be graphitized by e-beam treatment at 500°C, demonstrating promising applications in photolithography of graphene nanoarchitectures. Our results present UV-induced reactions on insulators for the formation of all sp2-carbon architectures, thereby converging top-down lithography and bottom-up on-surface chemistry into technology.

  • 30.
    Rastgoo Lahrood, Atena
    et al.
    Technical University of Munich, Germany; Nanosyst Initiat Munich, Germany; Centre NanoScience, Germany.
    Björk, Jonas
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, Faculty of Science & Engineering.
    Heckl, Wolfgang M.
    Technical University of Munich, Germany; Nanosyst Initiat Munich, Germany; Centre NanoScience, Germany; Deutsch Museum, Germany.
    Lackinger, Markus
    Technical University of Munich, Germany; Nanosyst Initiat Munich, Germany; Centre NanoScience, Germany; Deutsch Museum, Germany.
    1,3-Diiodobenzene on Cu(111) - an exceptional case of on-surface Ullmann coupling2015In: Chemical Communications, ISSN 1359-7345, E-ISSN 1364-548X, Vol. 51, no 68, p. 13301-13304Article in journal (Refereed)
    Abstract [en]

    Ullmann coupling of 1,3-diiodobenzene is studied on Cu(111) surfaces in ultra-high vacuum (UHV). In situ Scanning Tunneling Microscopy (STM) at room temperature revealed an unexpected ordered arrangement of highly uniform reaction products adsorbed atop a closed iodine monolayer.

  • 31.
    Robin, Abel
    et al.
    University of Liverpool, UK.
    Marnell, Lisa
    University of Liverpool, UK.
    Björk, Jonas
    University of Liverpool, UK.
    Dyer, Matthew S.
    University of Liverpool, UK.
    Bermudez, Phaedra Silva
    University of Liverpool, UK.
    Haq, Sam
    University of Liverpool, UK.
    Barrett, Steve
    University of Liverpool, UK.
    Persson, Mats
    University of Liverpool, UK.
    Minoia, Andrea
    University of Mons-Hainaut/Materia Nova, Mons, Belgium.
    Lazzorini, Roberto
    University of Mons-Hainaut/Materia Nova, Mons, Belgium.
    Raval, Rasmita
    University of Liverpool, UK.
    Adsorption and Organization of the Organic Radical 3-Carboxyproxyl on a Cu(110) Surface: A Combined STM, RAIRS, and DFT Study2009In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 113, no 30, p. 13223-13230Article in journal (Refereed)
    Abstract [en]

    We report on a combined experimental and theoretical study of the adsorption of the paramagnetic organic radical 2,2,5,5-tetramethyl-3-carboxypyrrolidine nitroxide (3-carboxyproxyl, 3CP) on a Cu(110) surface. Information from scanning tunneling microscopy (STM), reflection absorption infrared spectroscopy, and periodic density functional theory (DFT) calculations reveals important insights into the nature of the molecule-metal interface. We find that the molecule is robustly anchored to the surface via the formation of two Cu-O bonds between the carboxylate functionality and specific short-bridge adsorption sites on the Cu(110) surface. The adsorbed organic radicals appear in STM as discrete entities on the surface and can be imaged with submolecular resolution. We observe a tendency for local 2D ordering. Importantly, 3CP molecules adopt a preferred site, dictated by the strong interaction of the carboxylate groups and the steric repulsion of the methyl groups with the surface which orient the molecular ring almost perpendicular with respect to the surface. This conformation forces the NO radical away from the surface, and DFT calculations provide strong indications for the survival of the unpaired spin localized on the NO radical.

  • 32.
    Salinas, Borja Cirera
    et al.
    Technische Universität München, Garching, Germany.
    Zhang, Yi-Qi
    Technische Universität München, Garching, Germany.
    Björk, Jonas
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Klyatskaya, Svetlana
    Karlsruhe Institute of Technology, Garching, Germany.
    Chen, Zhi
    Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany.
    Ruben, Mario
    Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany.
    Barth, Johannes V.
    Technische Universität München, Garching, Germany.
    Klappenberger, Florian
    Technische Universität München, Garching, Germany.
    Synthesis of Extended Graphdiyne Wires by Vicinal Surface Templating2014In: Nano letters (Print), ISSN 1530-6984, E-ISSN 1530-6992, Vol. 14, no 4, p. 1891-1897Article in journal (Refereed)
    Abstract [en]

    Surface-assisted covalent synthesis currently evolves into an important approach for the fabrication of functional nanostructures at interfaces. Here, we employ scanning tunneling microscopy to investigate the homo-coupling reaction of linear, terminal alkyne-functionalized polyphenylene building-blocks on noble metal surfaces under ultra-high vacuum. On the flat Ag(111) surface thermal activation triggers a variety of side-reactions resulting in irregularly-branched polymeric networks. Upon alignment along the step-edges of the Ag(877) vicinal surface drastically improves the chemoselectivity of the linking process permitting the controlled synthesis of extended-graphdiyne wires with lengths reaching 30 nm. The ideal hydrocarbon scaffold is characterized by density functional theory as a 1D, direct band gap semiconductor material with both HOMO and LUMO-derived bands promisingly isolated within the electronic structure. The templating approach should be applicable to related organic precursors and different reaction schemes thus bears general promise for the engineering of novel low-dimensional carbon-based materials.

  • 33.
    Shchyrba, Aneliia
    et al.
    University of Basel, Switzerland .
    Waeckerlin, Christian
    Paul Scherrer Institute, Villigen, Switzerland .
    Nowakowski, Jan
    Paul Scherrer Institute, Villigen, Switzerland .
    Nowakowska, Sylwia
    University of Basel, Switzerland .
    Björk, Jonas
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Fatayer, Shadi
    University of Basel, Switzerland .
    Girovsky, Jan
    Paul Scherrer Institute, Villigen, Switzerland .
    Nijs, Thomas
    University of Basel, Switzerland .
    Martens, Susanne C.
    University of Basel, Switzerland; Heidelberg University, Germany .
    Kleibert, Armin
    Paul Scherrer Institute, Villigen, Switzerland .
    Stoehr, Meike
    University of Groningen, Netherlands .
    Ballav, Nirmalya
    Indian Institute of Science Education and Research, Pune, India.
    Jung, Thomas A.
    Paul Scherrer Institute, Villigen, Switzerland .
    Gade, Lutz H.
    Heidelberg University, Germany .
    Controlling the dimensionality of on-surface coordination polymers via endo- or exoligation2014In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 136, no 26, p. 9355-9363Article in journal (Refereed)
    Abstract [en]

    The formation of on-surface coordination polymers is controlled by the interplay of chemical reactivity and structure of the building blocks, as well as by the orientating role of the substrate registry. Beyond the predetermined patterns of structural assembly, the chemical reactivity of the reactants involved may provide alternative pathways in their aggregation. Organic molecules, which are transformed in a surface reaction, may be subsequently trapped via coordination of homo- or heterometal adatoms, which may also play a role in the molecular transformation. The amino-functionalized perylene derivative, 4,9-diaminoperylene quinone-3,10-diimine (DPDI), undergoes specific levels of dehydrogenation (-1 H-2 or -3 H-2) depending on the nature of the present adatoms (Fe, Co, Ni or Cu). In this way, the molecule is converted to an endo- or an exoligand, possessing a concave or convex arrangement of ligating atoms, which is decisive for the formation of either ID or 2D coordination polymers.

  • 34.
    Szekrényes, Zsolt
    et al.
    Institute for Solid State Physics and Optics, Wigner Research Centre for Physics, Hungarian Academy of Sciences, Hungary, Budapest.
    Kamarás, Katalin
    Institute for Solid State Physics and Optics, Wigner Research Centre for Physics, Hungarian Academy of Sciences, Hungary, Budapest.
    Tarczay, György
    Laboratory of Molecular Spectroscopy, Institute of Chemistry, Eötvös Loránd University, H-1518 Budapest, Hungary.
    Llanes-Pallás, Anna
    Dipartimento di Scienze Farmaceutiche and INSTM UdR di Trieste, Università degli Studi di Trieste, Piazzale Europa 1, 34127 Trieste, Italy.
    Marangoni, Tomas
    Dipartimento di Scienze Farmaceutiche and INSTM UdR di Trieste, Università degli Studi di Trieste, Piazzale Europa 1, 34127 Trieste, Italy.
    Prato, Maurizio
    Dipartimento di Scienze Farmaceutiche and INSTM UdR di Trieste, Università degli Studi di Trieste, Piazzale Europa 1, 34127 Trieste, Italy.
    Bonifazi, Davide
    Department of Chemistry, University of Namur (FUNDP), Rue de Bruxelles 61, 5000 Namur, Belgium.
    Björk, Jonas
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Hanke, Felix
    Surface Science Research Centre, University of Liverpool, UK.
    Persson, Mats
    Surface Science Research Centre, University of Liverpool, UK.
    Melting of Hydrogen Bonds in Uracil Derivatives Probed by Infrared Spectroscopy and ab Initio Molecular Dynamics2012In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 116, no 15, p. 4626-4633Article in journal (Refereed)
    Abstract [en]

    The thermal response of hydrogen bonds is a crucial aspect in the self-assembly of molecular nanostructures. To gain a detailed understanding of their response, we investigated infrared spectra of monomers and hydrogen-bonded dimers of two uracil-derivative molecules, supported by density functional theory calculations. Matrix isolation spectra of monomers, temperature dependence in the solid state, and ab initio molecular dynamics calculations give a comprehensive picture about the dimer structure and dynamics of such systems as well as a proper assignment of hydrogen-bond affected bands. The evolution of the hydrogen bond melting is followed by calculating the C═O···H–N distance distributions at different temperatures. The result of this calculation yields excellent agreement with the H-bond melting temperature observed by experiment.

  • 35.
    Yang, Biao
    et al.
    Soochow University, Peoples R China.
    Björk, Jonas
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, Faculty of Science & Engineering.
    Lin, Haiping
    Soochow University, Peoples R China.
    Zhang, Xiaoqing
    Soochow University, Peoples R China.
    Zhang, Haiming
    Soochow University, Peoples R China.
    Li, Youyong
    Soochow University, Peoples R China.
    Fan, Jian
    Soochow University, Peoples R China.
    Li, Qing
    Soochow University, Peoples R China.
    Chi, Lifeng
    Soochow University, Peoples R China.
    Synthesis of Surface Covalent Organic Frameworks via Dimerization and Cyclotrimerization of Acetyls2015In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 137, no 15, p. 4904-4907Article in journal (Refereed)
    Abstract [en]

    The formation of additional phenyl rings on surfaces is of particular interest because it allows for the building-up of surface covalent organic frameworks. In this work, we show for the first time that the cyclotrimerization of acetyls to aromatics provides a promising approach to 2D conjugated covalent networks on surfaces under ultrahigh vacuum. With the aid of scanning tunneling microscopy, we have systematically studied the reaction pathways and the products. With the combination of density functional theory calculations and X-ray photoemission spectroscopy, the surface-assisted reaction mechanism, which is different from that in solution, was explored.

  • 36.
    Zhang, Yi-Qi
    et al.
    Technical University of Munich, Germany.
    Björk, Jonas
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, Faculty of Science & Engineering.
    Barth, Johannes V.
    Technical University of Munich, Germany.
    Klappenberger, Florian
    Technical University of Munich, Germany.
    Intermolecular Hybridization Creating Nanopore Orbital in a Supramolecular Hydrocarbon Sheet2016In: Nano letters (Print), ISSN 1530-6984, E-ISSN 1530-6992, Vol. 16, no 7, p. 4274-4281Article in journal (Refereed)
    Abstract [en]

    Molecular orbital engineering is a key ingredient for the design of organic devices. Intermolecular hybridization promises efficient charge carrier transport but usually requires dense packing for significant wave function overlap. Here we use scanning tunneling spectroscopy to spatially resolve the electronic structure of a surface-confined nanoporous supramolecular sheet of a prototypical hydrocarbon compound featuring terminal alkyne (CCH) groups. Surprisingly, localized nanopore orbitals are observed, with their electron density centered in the cavities surrounded by the functional moieties. Density functional theory calculations reveal that these new electronic states originate from the intermolecular hybridization of six in-plane x-orbitals of the carbon carbon triple bonds, exhibiting significant electronic splitting and an energy downshift of approximately 1 eV. Importantly, these nanopore states are distinct from previously reported interfacial states. We unravel the underlying connection between the formation of nanopore orbital and geometric arrangements of functional groups, thus demonstrating the generality of applying related orbital engineering concepts in various types of porous organic structures.

  • 37.
    Zhang, Yi-Qi
    et al.
    Technical University of Munich, Germany.
    Björk, Jonas
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, Faculty of Science & Engineering.
    Weber, Peter
    Technical University of Munich, Germany.
    Hellwig, Raphael
    Technical University of Munich, Germany.
    Diller, Katharina
    Technical University of Munich, Germany.
    Papageorgiou, Anthoula C.
    Technical University of Munich, Germany.
    Cheol Oh, Seung
    Technical University of Munich, Germany.
    Fischer, Sybille
    Technical University of Munich, Germany.
    Allegretti, Francesco
    Technical University of Munich, Germany.
    Klyatskaya, Svetlana
    Karlsruhe Institute Technology, Germany.
    Ruben, Mario
    Karlsruhe Institute Technology, Germany; University of Strasbourg, France.
    Barth, Johannes V.
    Technical University of Munich, Germany.
    Klappenberger, Florian
    Technical University of Munich, Germany.
    Unusual Deprotonated Alkynyl Hydrogen Bonding in Metal-Supported Hydrocarbon Assembly2015In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 119, no 17, p. 9669-9679Article in journal (Refereed)
    Abstract [en]

    We demonstrate that terminal alkynyl moieties represent powerful functional groups for driving thermally stable, on-surface supramolecular structure formation on a reactive substrate. Through a combination of scanning tunneling microscopy, X-ray photoelectron spectroscopy, near-edge X-ray absorption-fine-structure spectroscopy and density functional theory calculations, we investigate the molecule-surface interaction and self-assembly of two prototypical hydrocarbon species on Cu(111). For 1,3,5-tris(4-ethynylphenyl)benzene (Ext-TEB) adsorption at low temperature (200 K) results in nonassembling, conformationally adapted intact species. Deprotonation of the terminal alkyne moieties, taking place at temperatures ranging from 300 to 350 K, triggers the formation of room-temperature stable, close-packed supramolecular islands. Through DFT calculations, the stabilizing interaction is identified as a trifurcated ionic C-H center dot center dot center dot pi(-delta) hydrogen bonding between the g-system of the ionic alkynyl groups and methine moieties of nearby benzene rings, providing an energy gain of 0.26 eV/molecule upon network formation. Robust assemblies result from the combination of this weak directional attraction with the strong surface anchoring also provided by the alkynyl groups. The generality of this novel ionic hydrogen-bonding type is demonstrated by the observation of low-dimensional assemblies of 9,10-diethynyl-anthracene on the same surface, consistently explained with the same type of interaction.

  • 38.
    Zhang, Yi-Qi
    et al.
    Technische Universität München, Garching, Germany.
    Kepčija, Nenad
    Technische Universität München, Garching, Germany.
    Kleinschrodt, Martin
    Technische Universität München, Garching, Germany.
    Diller, Katharina
    Technische Universität München, Garching, Germany.
    Fischer, Sybille
    Technische Universität München, Garching, Germany.
    Papageorgiou, Anthoula C.
    Technische Universität München, Garching, Germany.
    Allegretti, Francesco
    Technische Universität München, Garching, Germany.
    Björk, Jonas
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Klyatskaya, Svetlana
    Institute of Nanotechnology (INT), Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany.
    Klappenberger, Florian
    Technische Universität München, Garching, Germany.
    Ruben, Mario
    Institute of Nanotechnology (INT), Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany.
    Barth, Johannes V.
    Technische Universität München, Garching, Germany.
    Homo-coupling of terminal alkynes on a noble metal surface2012In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 3Article in journal (Refereed)
    Abstract [en]

    The covalent linking of acetylenes presents an important route for the fabrication of novel carbon-based scaffolds and two-dimensional materials distinct from graphene. To date few attempts have been reported to implement this strategy at well-defined interfaces or monolayer templates. Here we demonstrate through real space direct visualization and manipulation in combination with X-ray photoelectron spectroscopy and density functional theory calculations the Ag surface-mediated terminal alkyne Csp−H bond activation and concomitant homo-coupling in a process formally reminiscent of the classical Glaser–Hay type reaction. The alkyne homo-coupling takes place on the Ag(111) noble metal surface in ultrahigh vacuum under soft conditions in the absence of conventionally used transition metal catalysts and with volatile H2 as the only by-product. With the employed multitopic ethynyl species, we demonstrate a hierarchic reaction pathway that affords discrete compounds or polymeric networks featuring a conjugated backbone. This presents a new approach towards on-surface covalent chemistry and the realization of two-dimensional carbon-rich or all-carbon polymers.

1 - 38 of 38
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