Self-aligning atomic strings in surface-supported biomolecular gratings

Schiffrin, Agustin; Reichert, Joachim; Auwärter, Willi; Jahnz, G.; Pennec, Yan; Weber‐Bargioni, Alexander; Stepanyuk, V. S.; Niebergall, L.; Bruno, P.; Barth, Johannes V.

doi:10.1103/physrevb.78.035424

Cited by 54 publications

(53 citation statements)

References 42 publications

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“…33; however, with this system, the flexibility of the constituting porphyrins plays an important role. A potential pathway that could mediate a correlated dynamics is given by the indirect electronic interactions due to surface state scattering on the network and confined objects, which has been exploited to steer the alignment of adatoms in supramolecular gratings on the same substrate in the past (34,35). However, with these systems, there was similarly no evidence for a correlated translational motion or lateral organization in adjacent 1D furrows (34,35), presumably because there is little crosstalk between areas separated by molecular rims (34)(35)(36).…”

Section: Resultsmentioning

confidence: 85%

Rotational and constitutional dynamics of caged supramolecules

Kühne

Klappenberger²,

Krenner³

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

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The confinement of molecular species in nanoscale environments leads to intriguing dynamic phenomena. Notably, the organization and rotational motions of individual molecules were controlled by carefully designed, fully supramolecular host architectures. Here we use an open 2D coordination network on a smooth metal surface to steer the self-assembly of discrete trimeric guest units, identified as noncovalently bound dynamers. Each caged chiral supramolecule performs concerted, chirality-preserving rotary motions within the template honeycomb pore, which are visualized and quantitatively analyzed using temperature-controlled scanning tunneling microscopy. Furthermore, with higher thermal energies, a constitutional system dynamics appears, which is revealed by monitoring repetitive switching events of the confined supramolecules' chirality signature, reflecting decay and reassembly of the caged units. supramolecular dynamics | nanochemistry | surface architecture T he dynamics of molecular species can be controlled by carefully designed, fully supramolecular host architectures, provided either as discrete capsules or extended nanoporous networks. It was recognized in particular that unique rotary motion phenomena of single molecular species can be encoded by such conditions (1-5). Moreover, with the restriction to surfaceconfined systems it became possible to investigate molecular rotation and noncovalent assembly processes of individual molecules adsorbed at surfaces by atomic-scale scanning tunneling microscopy (STM) (6-12). However, the direct observation of dynamic supramolecular entities in controlled environments remained elusive although this objective represents a key issue of supramolecular science and constitutional dynamic chemistry (13-16). Herein we report dynamic phenomena at the supramolecular level, resulting from the nanoscale confinement of a multicomponent aggregate in an open 2D coordination network on a smooth metal surface. The presented nanopores steer the assembly and cage the realized discrete 2D-chiral trimeric dynamers, whose behavior is directly monitored by temperaturecontrolled STM. We visualized and analyzed quantitatively their rotary motions, whereby the collective nature of the system dynamics is demonstrated by following chirality-preserving individual reorientation events. The findings reveal opportunities for the field of surface-mounted rotors, limited to single molecular units so far (17)(18)(19). Furthermore, we infer constitutional dynamics from the switching of the chirality signature for increased thermal energies, reflecting the repetitive decay and reassembly of the caged supramolecules. With our observations, a demonstrator for the intricate collective dynamics of caged supramolecular dynamers is provided.

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Section: Resultsmentioning

confidence: 85%

Rotational and constitutional dynamics of caged supramolecules

Kühne

Klappenberger²,

Krenner³

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

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“…[1][2][3][4][5][6][7][8][9][10][11][12] Some organic molecules have the ability to self-assemble in two-dimensional ͑2D͒ networks when they are deposited on a surface. Some properties of these templates, such as their possibility to form either chiral or non-chiral ordered structures, 13,14 have been intensively studied for understanding their possible applications in nanotechnology ͑e.g., Refs.…”

Section: Introductionmentioning

confidence: 99%

Experimental and theoretical analysis of H-bonded supramolecular assemblies of PTCDA molecules

et al. 2010

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Physics, 81(19), 195412-1-195412-11. [195412]. https://doi.org/10.1103/PhysRevB. 81.195412 Copyright Other than for strictly personal use, it is not permitted to download or to forward/distribute the text or part of it without the consent of the author(s) and/or copyright holder(s), unless the work is under an open content license (like Creative Commons).Take-down policy If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim.Downloaded from the University of Groningen/UMCG research database (Pure): http://www.rug.nl/research/portal. For technical reasons the number of authors shown on this cover page is limited to 10 maximum. Using a systematic method based on considering all possible hydrogen bond connections between molecules and subsequent density-functional theory ͑DFT͒ calculations, we investigated planar superstructures that the perylene-3,4,9,10-tetracarboxylic-3,4,9,10-dianhydride ͑PTCDA͒ molecules can form in one and two dimensions. Structures studied are mostly based on two molecule unit cells and all assemble in flat periodic arrays. We show that 42 different monolayer structures are possible, which can be split into eight families of distinct structures. A single representative of every family was selected and relaxed using DFT. We find square, herringbone and brick wall phases ͑among others͒ which were already observed on various substrates. Using scanning tunneling microscopy in ultrahigh vacuum, we also observed herringbone and square phases after sublimation of PTCDA molecules on the Au͑111͒ surface at room temperature, the square phase being observed for the first time on this substrate. The square phase appears as a thin stripe separating two herringbone domains and provides a perfect structural matching for them. A similar structural formation serving as a domain wall between two other phases has been recently reported on the same surface formed by melamine molecules ͓F. Silly et al., J. Phys. Chem. C 112, 11476 ͑2008͔͒. Our theoretical analysis helps to account for these and other observed complex structures.

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“…40,41 Earlier studies have already demonstrated that metallic substrates can indeed mediate long-range interactions and influence atomic and molecular ordering. Examples include shells of atoms, 41 zwitterionic nano gratings, 42 the self-aligned atomic strings in bimolecular gratings, 43 and porous networks of anthraquinone molecules. 44 Reported energies for substratemediated interactions are of the order of one or more milli electron volts over a distance of a few nanometers (see overview in Ref.…”

Section: Long-range Surface-mediated Interactionsmentioning

confidence: 99%

Self-assembly of strongly dipolar molecules on metal surfaces

Kunkel

Hooper

Simpson

et al. 2015

The Journal of Chemical Physics

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The role of dipole-dipole interactions in the self-assembly of dipolar organic molecules on surfaces is investigated. As a model system, strongly dipolar model molecules, p-benzoquinonemonoimine zwitterions (ZI) of type C 6 H 2 (· · · NHR) 2 (· · · O) 2 on crystalline coinage metal surfaces were investigated with scanning tunneling microscopy and first principles calculations. Depending on the substrate, the molecules assemble into small clusters, nano gratings, and stripes, as well as in two-dimensional islands. The alignment of the molecular dipoles in those assemblies only rarely assumes the lowest electrostatic energy configuration. Based on calculations of the electrostatic energy for various experimentally observed molecular arrangements and under consideration of computed dipole moments of adsorbed molecules, the electrostatic energy minimization is ruled out as the driving force in the self-assembly. The structures observed are mainly the result of a competition between chemical interactions and substrate effects. The substrate's role in the self-assembly is to (i) reduce and realign the molecular dipole through charge donation and back donation involving both the molecular HOMO and LUMO, (ii) dictate the epitaxial orientation of the adsorbates, specifically so on Cu(111), and (iii) inhibit attractive forces between neighboring chains in the system ZI/Cu(111), which results in regularly spaced molecular gratings. C 2015 AIP Publishing LLC. [http://dx

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Self-aligning atomic strings in surface-supported biomolecular gratings

Cited by 54 publications

References 42 publications

Rotational and constitutional dynamics of caged supramolecules

Rotational and constitutional dynamics of caged supramolecules

Experimental and theoretical analysis of H-bonded supramolecular assemblies of PTCDA molecules

Self-assembly of strongly dipolar molecules on metal surfaces

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