Structure, registry and imaging mechanism of alkylcyanobiphenyl molecules by tunnelling microscopy

Smith, D. P. E.; Hörber, J. K. H.; Binnig, G.; Nejoh, H.

doi:10.1038/344641a0

Cited by 288 publications

(122 citation statements)

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“…Periodic dislocations observed in the crystal structures were explained on the basis of strong molecule-substrate interactions and the registry mechanism of the alkyl chains with the underlying substrate. [55] Thus, on the basis of these literature reports, we can explain the discontinuous lamellar features observed in the present case as follows. A major flaw in the schematic displayed in Figure 2a is that it does not take into consideration the influence of the substrate lattice on the self-assembling pattern.…”

Section: Resultsmentioning

confidence: 69%

Hydrogen Bonding Versus van der Waals Interactions: Competitive Influence of Noncovalent Interactions on 2D Self‐Assembly at the Liquid–Solid Interface

Mali

Lava

Binnemans

et al. 2010

Chemistry A European J

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The structures of the self-assembled monolayers of various 4-alkoxybenzoic acids physisorbed at the liquid-solid interface were established by employing scanning tunnelling microscopy (STM). This study has been essentially undertaken to explore the competitive influence of van der Waals and hydrogen-bonding interactions on the process of two-dimensional self-assembly. These acid derivatives form hydrogen-bonded dimers as expected; however, the dimers organise themselves in the form of relatively complex lamellae. The characteristic feature of these lamellae is the presence of regular discommensurations or kinks along the lamella propagation direction. The formation of kinked lamellae is discussed in light of the registry mechanism of the alkyl chains with the underlying graphite substrate. The location of the kinks along a lamella depends on the number (odd or even) of carbon atoms in the alkyl chain. This result indicates that concerted van der Waals interactions of the alkyl chain units introduce the odd/even chain-length effect on the surface-assembled supramolecular patterns. The odd/even effects are retained even upon complexation with a hydrogen-bond acceptor. However, as the solvent is changed from 1-phenyloctane to 1-octanoic acid, the kinked lamellae as well as the odd/even effects disappear. This solvent-induced convergence of supramolecular patterns is attained by means of co-crystallisation of octanoic acid molecules in the 2D crystal lattice, which is evident from high-resolution STM images. The solvent co-adsorption phenomenon is discussed in terms of competing van der Waals and hydrogen-bonding interactions.

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Section: Resultsmentioning

confidence: 69%

Hydrogen Bonding Versus van der Waals Interactions: Competitive Influence of Noncovalent Interactions on 2D Self‐Assembly at the Liquid–Solid Interface

Mali

Lava

Binnemans

et al. 2010

Chemistry A European J

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“…The Scanning Tunneling Microscope (STM) [9] permits one to resolve at the atomic level crystallographic structures [10] and organic molecules [11]. The Atomic Force Microscope (AFM) [12] has been successfully employed to study biological and nano-fabricated structures, overcoming the diffraction limit of optical microscopes.…”

Section: Introductionmentioning

confidence: 99%

Brownian motion in a nonhomogeneous force field and photonic force microscope

Volpe

Petrov

2007

Phys. Rev. E

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The Photonic Force Microscope (PFM) is an opto-mechanical technique based on an optical trap that can be assumed to probe forces in microscopic systems. This technique has been used to measure forces in the range of pico-and femto-Newton, assessing the mechanical properties of biomolecules as well as of other microscopic systems. For a correct use of the PFM, the force field to measure has to be invariable (homogeneous) on the scale of the Brownian motion of the trapped probe. This condition implicates that the force field must be conservative, excluding the possibility of a rotational component. However, there are cases where these assumptions are not fulfilled Here, we show how to improve the PFM technique in order to be able to deal with these cases. We introduce the theory of this enhanced PFM and we propose a concrete analysis workflow to reconstruct the force field from the experimental time-series of the probe position. Furthermore, we experimentally verify some particularly important cases, namely the case of a conservative or rotational force-field.

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“…No signs of mobility were observed during investigations, which lasted up to 1 h in a single region. That such an array can form is probably due to the intermolecular hydrogen bonding capability of the DNA bases (4).Ordered molecular layers of organic molecules, such as benzene (5), alkanes (6), or liquid crystals (7,8), are the most prominent examples to have been imaged recently by STM at atomic resolution. STM results of adenine, one of the four DNA bases, have recently been obtained on graphite by Allen et al (9).…”

mentioning

confidence: 99%

Two-dimensional ordering of the DNA base guanine observed by scanning tunneling microscopy.

Heckl

Smith

Binnig

et al. 1991

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

142

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Guanine, one ofthe four DNA bases, has been observed by tunneling microscopy to form a two-dimensional ordered structure on two crystalline substrates, graphite and MoS2. The two-dimensional lattice formed by guanine is nearly identical on the two surfaces, and heteroepitaxy appears to be the growth mechanism in both cases. Although the resolution of molecular details is superior for the graphite substrate, the simpler results on MoS2 are not only easier to interpret but also facilitate the understanding of the more complex images on graphite. We propose that the interfacial structure is composed of linear chains of hydrogen-bonded molecules aligned into a closely packed two-dimensional array.Several recent studies have examined the possibility of imaging DNA by scanning tunneling microscopy (STM) (1-3). However, the ultimate goal-to read the code contained in the strands-has not yet been achieved. To do so it must be possible to recognize clearly and distinguish between the four bases of the genetic code. One essential requirement for imaging small organic molecules by STM is to find experimental preparation conditions whereby the molecules stick firmly to the substrate and form a highly stable layer. This is necessary to withstand the forces of the STM tip during imaging. Compared to the binding of complete DNA strands to the basal planes of MoS2 or graphite, the adsorption of "naked" nucleotide bases is favored by their greater hydrophobicity and, as is shown in this report, by their ability to register with the substrate, thus forming a stable twodimensional ordered array. No signs of mobility were observed during investigations, which lasted up to 1 h in a single region. That such an array can form is probably due to the intermolecular hydrogen bonding capability of the DNA bases (4).Ordered molecular layers of organic molecules, such as benzene (5), alkanes (6), or liquid crystals (7,8), are the most prominent examples to have been imaged recently by STM at atomic resolution. STM results of adenine, one of the four DNA bases, have recently been obtained on graphite by Allen et al. (9). Using a sample preparation technique similar to theirs (9), we prepared samples of guanine on the surfaces of natural MoS2 crystals and highly oriented pyrolytic graphite. We often observed steps from the bare substrate to monolayers of guanine. The results presented in this paper were obtained on such monolayer islands. The character of the steplines provides additional information since the orientation of the molecular lattice with respect to the substrate can be measured there. In the STM images the bases look quite different depending on whether they are deposited on MoS2 (Fig. 1) or on graphite (see Fig. 3). The main differences are that on MoS2 the bases appear as distinct well-isolated nearly structureless blobs; on graphite more details become visible, although it is still not possible to determine the 8003The publication costs of this article were defrayed in part by page charge payment. This article must ...

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Structure, registry and imaging mechanism of alkylcyanobiphenyl molecules by tunnelling microscopy

Cited by 288 publications

References 10 publications

Hydrogen Bonding Versus van der Waals Interactions: Competitive Influence of Noncovalent Interactions on 2D Self‐Assembly at the Liquid–Solid Interface

Hydrogen Bonding Versus van der Waals Interactions: Competitive Influence of Noncovalent Interactions on 2D Self‐Assembly at the Liquid–Solid Interface

Brownian motion in a nonhomogeneous force field and photonic force microscope

Two-dimensional ordering of the DNA base guanine observed by scanning tunneling microscopy.

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