Dynamics of Thioether Molecular Rotors: Effects of Surface Interactions and Chain Flexibility

Tierney, Heather L.; Baber, Ashleigh E.; Sykes, E. Charles H.; Akimov, Alexey V.; Kolomeisky, Anatoly B.

doi:10.1021/jp9017844

Cited by 36 publications

(80 citation statements)

References 46 publications

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“…As reported in previous work by this group, isolated DBS molecules behaved as molecular rotors on Au{111}. [22][23][24]42,43 The central sulfur atom acted as an anchor and the alkyl tails rotated between three high symmetry directions; at 78 K the rotation was significantly faster than the STM imaging rate (∼2 min per image), and the molecules appeared hexagonal in shape, as depicted in Figure 2A. Furthermore, the molecules rotated at a rate significantly greater than that of translational motion, as evidenced by STM movies acquired at 78 K, in which rotating molecules did not diffuse more than a few lattice spacings throughout the movie taken over several hours (see Supporting Information).…”

Section: Resultssupporting

confidence: 73%

“…15, 16 More recent studies, however, have conclusively shown that thioethers with tails up to 18 carbons in length adsorb with their alkyl tails parallel to the surface. [17][18][19][20][21][22][23][24] As such, adjusting side chain length may enable control over lateral spacing. It has also been debated whether thioether species dissociate upon adsorption via cleavage of a S-C bond, 25 but it is now accepted that these species adsorb intact.…”

Section: Introductionmentioning

confidence: 99%

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Adsorption, Assembly, and Dynamics of Dibutyl Sulfide on Au{111}

et al. 2010

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Alkanethiol (RSH) monolayers are by far the most extensively studied surface self-assembly systems due to their robustness and the opportunity to control their assembly in the dimension perpendicular to the surface. Thioethers (RSR′), a similar class of molecule, remain largely unstudied to date but may offer a similar level of assembly control parallel to the surface. Here we report the self-assembly of dibutyl sulfide, a symmetric thioether species, on a Au{111} surface using scanning tunneling microscopy. As with thiols, dibutyl sulfide forms well-ordered monolayers, but due to the slightly weaker molecule-metal bond, the coverage and temperature-dependent behavior is very different than that of alkanethiols. Adsorption is sensitive to the different regions of the Au{111} herringbone reconstruction. Dibutyl sulfide lies parallel to the surface and forms well-ordered chains in domains that preferentially bind first in fcc regions, then hcp, and finally on soliton walls. The sulfide-Au interaction is strong enough to disrupt the native herringbone reconstruction of Au; however, unlike thiols, dibutyl sulfide adsorption does not result in etch pit formation. A monolayer of dibutyl sulfide has a very low defect density as compared to thiol-SAM based systems. This low defect density hints at the possibility of using a thioether moiety as a basis for a self-assembled system free of typical defects like etch pits, which allow attack and degradation of the monolayer. Upon annealing the surface with a high molecular coverage to 575 K, dibutyl sulfide desorbs molecularly from the less energetically favorable regions of the surface first. At this reduced coverage the system returns to an intermediate-coverage structure, thereby demonstrating the reversibility of the assembly. Elevating the temperature further causes the entire monolayer to desorb, and the original herringbone structure of Au returns. We postulate that this reversibility, coupled with the high rate of concerted rearrangements, allows this system to reach a very high level of order.

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Section: Resultssupporting

confidence: 73%

Section: Introductionmentioning

confidence: 99%

Adsorption, Assembly, and Dynamics of Dibutyl Sulfide on Au{111}

et al. 2010

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“…The molecule ends in conformation f2cg at I Set ¼ 0:5 nA. Recent publications have shown that a configurational change of a molecule on a metal surface can be imaged by STM [25,26] and that a rotation of molecules in an increasing electric field can be monitored by a sequence of STM images [27]. Consequently, the change of electronic properties related to different adsorption geometries can be monitored by STS, as reported in this work.…”

Section: Prl 105 066801 (2010) P H Y S I C a L R E V I E W L E T T Ementioning

confidence: 61%

Electronic Mapping of Molecular Orbitals at the Molecule-Metal Interface

et al. 2010

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The molecule-metal interface formed by pyridine-2,5-dicarboxylic acid chemically bonded to the Cu (110) surface is investigated by scanning tunneling microscopy and first-principles calculations. Our current-voltage spectroscopy studies reveal an electronic mapping of molecular orbitals as a function of tip position. By combining experimental and theoretical investigations, individual molecular orbitals are characterized by their energy and spatial distribution. The importance of adsorption geometries and conformational changes on the electron transport properties is highlighted. DOI: 10.1103/PhysRevLett.105.066801 PACS numbers: 73.63.Àb, 31.15.AÀ, 68.37.Ef, 82.37.Gk In the past decade, we have witnessed significant progress in integrating organic molecules in functional molecular devices like single molecule diodes [1,2] or in organic field-effect transistors [3,4]. To improve the functionality of such molecular electronic devices, an essential prerequisite is to gain a substantial understanding of the electronic structure of molecule-surface interfaces near the Fermi level that ultimately controls the performance of such a device [5][6][7].In this context, the precise energetic alignment of the molecular orbitals with respect to the Fermi level of the substrate, in particular, that of the highest occupied molecular orbitals and the lowest unoccupied molecular orbitals, is a key component of the electronic structure of the molecule-surface system under consideration. Therefore, in this Letter we present a detailed electronic mapping of molecular orbitals (MOs) by distance-dependent currentvoltage (I-V) spectroscopy. Combining the spatially resolved scanning tunneling spectroscopy (STS) results with density functional theory (DFT) investigations, we show how to identify the electronic structure of a molecule chemically bonded to a metallic surface. As a model system we investigate the adsorption of the pyridine-2,5-dicarboxylic acid (PyDCAH 2 ) on Cu(110).Our ab initio total-energy calculations have been performed in the framework of DFT [8] by using the PerdewBurke-Ernzerhof [9] exchange-correlation energy functional as implemented in the VASP code [10,11]. A detailed description is available in the supplementary material [12]. We first note that, in the case of the PyDCAH 2 molecule, which adsorbs on the Cu(110) surface under deprotonation of one carboxyl group, forming PyDCAH, several different adsorption geometries must be taken into account due to the presence of a nitrogen atom in the aromatic ring. Therefore, we differentiate in the following between C 7 H 4 N ð2Þ O 4 , describing a PyDCAH molecule with the nitrogen on position two in the ring (counting the ring atoms from the carbon atom located at the bonded carboxylate unit), and C 7 H 4 N ð3Þ O 4 , denoted as configuration f1g and f2g, respectively. Experimentally, there is no possibility to influence the orientation of the molecule during the adsorption process or to monitor topographically which configuration is preferentially adsorbed. If the ...

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“…The surface was represented as a slab of 1067 gold atoms organized in 3 layers (surface plane 111) and their 2D replicas, thus effectively leading to quasi-infinite representation of the surface, similar to what was utilized in earlier studies 31. Two different surfaces Au (111) and Au (100) have been used in our calculations.…”

Section: Theoretical Calculationsmentioning

confidence: 99%

Dynamics of Single-Molecule Rotations on Surfaces that Depend on Symmetry, Interactions, and Molecular Sizes

Akimov

Kolomeisky

2010

J. Phys. Chem. C

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Rotating surface-mounted molecules have attracted attention of many research groups as a way to develop new nanoscale devices and materials. However, mechanisms of motion of these rotors at the single-molecule level are still not well understood. Theoretical and experimental studies on thioether molecular rotors on gold surfaces suggest that the size of the molecules, their flexibility and steric repulsions with the surface are important for dynamics of the system. A complex combination of these factors leads to the observation that the rotation speeds have not been hindered by increasing the length of the alkyl chains. However, experiments on diferrocene derivatives indicated that a significant increase in the rotational barriers for longer molecules. We present here a comprehensive theoretical study that combines molecular dynamics simulations and simple models to investigate what factors influence single-molecule rotations on the surfaces. Our results suggest that rotational dynamics is determined by the size and by the symmetry of the molecules and surfaces, and by interactions with surfaces. Our theoretical predictions are in excellent agreement with current experimental observations.

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Dynamics of Thioether Molecular Rotors: Effects of Surface Interactions and Chain Flexibility

Cited by 36 publications

References 46 publications

Adsorption, Assembly, and Dynamics of Dibutyl Sulfide on Au{111}

Adsorption, Assembly, and Dynamics of Dibutyl Sulfide on Au{111}

Electronic Mapping of Molecular Orbitals at the Molecule-Metal Interface

Dynamics of Single-Molecule Rotations on Surfaces that Depend on Symmetry, Interactions, and Molecular Sizes

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