| 1. |
- Björk, Jonas, et al.
(författare)
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Adsorption of Aromatic and Anti-Aromatic Systems on Graphene through π−π Stacking
- 2010
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Ingår i: The Journal of Physical Chemistry Letters. - : American Chemical Society (ACS). - 1948-7185. ; 1, s. 3407-3412
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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| 2. |
- Björk, Jonas, et al.
(författare)
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STM fingerprint of molecule-adatom interactions in a self-assembled metal-organic surface coordination network on Cu(111)
- 2010
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Ingår i: Physical Chemistry, Chemical Physics - PCCP. - : R S C Publications. - 1463-9076 .- 1463-9084. ; 12, s. 8815-8821
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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| 3. |
- Hanke, F., et al.
(författare)
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Structure and stability of weakly chemisorbed ethene adsorbed on low-index Cu surfaces: performance of density functionals with van der Waals interactions
- 2012
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Ingår i: Journal of Physics Condensed Matter. - : IOP Publishing. - 0953-8984 .- 1361-648X. ; 24:42, s. Article Number: 424217 -
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Tidskriftsartikel (refereegranskat)abstract
- We have investigated the performance of popular density functionals that include van der Waals interactions for the experimentally well-characterized problem of ethene (C2H4) 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.
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| 4. |
- Honkela, M. L., et al.
(författare)
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Computational study of the adsorption and dissociation of phenol on Pt and Rh surfaces
- 2012
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Ingår i: Physical Chemistry Chemical Physics. - : Royal Society of Chemistry (RSC). - 1463-9084 .- 1463-9076. ; 14:16, s. 5849-5854
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Tidskriftsartikel (refereegranskat)abstract
- 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).
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| 5. |
- Matena, Manfred, et al.
(författare)
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Aggregation and contingent metal/surface reactivity of 1,3,8,10-tetraazaperopyrene (TAPP) on Cu(111)
- 2010
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Ingår i: Chemistry - A European Journal. - : Wiley-VCH Verlagsgesellschaft. - 0947-6539 .- 1521-3765. ; 16:7, s. 2079-2091
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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| 6. |
- Matena, M., et al.
(författare)
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On-surface synthesis of a two-dimensional porous coordination network: Unraveling adsorbate interactions
- 2014
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Ingår i: Physical Review B - Condensed Matter and Materials Physics. - 2469-9950 .- 2469-9969. ; 90, s. 125408-125415
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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| 7. |
- Palma, Carlos-Andres, et al.
(författare)
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Tailoring Bicomponent Supramolecular Nanoporous Networks : Phase Segregation, Polymorphism, and Glasses at the Solid−Liquid Interface
- 2009
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Ingår i: Journal of the American Chemical Society. - : American Chemical Society (ACS). - 0002-7863 .- 1520-5126. ; 131:36, s. 13062-13071
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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| 8. |
- Robin, Abel, et al.
(författare)
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Adsorption and Organization of the Organic Radical 3-Carboxyproxyl on a Cu(110) Surface : A Combined STM, RAIRS, and DFT Study
- 2009
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Ingår i: The Journal of Physical Chemistry C. - : American Chemical Society (ACS). - 1932-7447 .- 1932-7455. ; 113:30, s. 13223-13230
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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| 9. |
- Szekrenyes, Z., et al.
(författare)
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Melting of Hydrogen Bonds in Uracil Derivatives Probed by Infrared Spectroscopy and ab Initio Molecular Dynamics
- 2012
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Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-5207 .- 1520-6106. ; 116:15, s. 4626-4633
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Tidskriftsartikel (refereegranskat)abstract
- 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 center dot center dot center dot H-N distance distributions at different temperatures. The result this calculation yields excellent agreement with the H-bond melting temperature observed by experiment.
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