Intermolecular Contrast in Atomic Force Microscopy Images without Intermolecular Bonds

Hämäläinen, Sampsa K.; Heijden, Nadine van der; Lit, Joost van der; Hartog, Stephan den; Liljeroth, Peter; Swart, Ingmar

doi:10.1103/physrevlett.113.186102

Cited by 136 publications

(124 citation statements)

References 28 publications

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“…[25][26][27] However, achieving high resolution in NC-AFM images at room temperature is still a challenge 28 and often the interpretation of images down to an atomistic level requires a detailed understanding of the tip-sample interactions. [29][30][31] Theoretical calculations can provide a better understanding of adsorption geometries, film structures and nucleation sites. Previous work on molecular adsorption on insulators using DFT has been often restricted to ground state calculations that represent a frozen 0 K system.…”

Section: -15mentioning

confidence: 99%

Calculating the Entropy Loss on Adsorption of Organic Molecules at Insulating Surfaces

et al. 2016

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Although it is recognized that dynamic behavior of adsorbing molecules strongly affects the entropic contribution to adsorption free energy, detailed studies of the adsorption entropy of large organic molecules at insulating surfaces are still rare. We compared adsorption of two different functionalized organic molecules, 1,3,5-tri-(4-cyano-4,4 biphenyl)-benzene (TCB) and 1,4-bis(cyanophenyl)-2,5-bis(decyloxy)benzene (CDB), on the KCl (001) surface using density functional theory (DFT) and molecular dynamics (MD) simulations. The accuracy of the van der Waals corrected DFT-D3 was benchmarked using Møller-Plesset perturbation theory calculations. Classical force fields were then parameterized for both the TCB and CDB molecules on the KCl (001) surface. These force fields were used to perform potential of mean force (PMF) calculations of adsorption of individual molecules and extract information on the entropic contributions to adsorption energy. The results demonstrate that entropy losses upon adsorption are significant for flexible molecules, such as considered here, and even at relatively low temperatures (e.g. 400 K) can match the enthalpy contribution to adsorption energy.

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Section: -15mentioning

confidence: 99%

Calculating the Entropy Loss on Adsorption of Organic Molecules at Insulating Surfaces

et al. 2016

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“…Another electrostatic model called the "virtual tip" method avoids the explicit modeling of the tip 20 . Simulation methods based on classical or Morse potentials 6,8,17,18,21 to describe the tip-sample interaction are not limited to electrostatic forces and are computationally light, but they may not be accurate enough for systems with chemically reactive tips. Quantum simulation methods 4,11,12,22 are thought to be the most accurate but are computationally intensive.…”

mentioning

confidence: 99%

Simulating contrast inversion in atomic force microscopy imaging with real-space pseudopotentials

2017

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“…Recently, this kind of intermolecular contrast in STM and NC-AFM images has been discussed for several systems. [27][28][29] Occasionally, we observe small defects along the molecular array in the form of missed bumps or extra STM signals either in the dark undulating stripes or in the double bumped wires (see Fig. 1e).…”

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confidence: 91%

On-surface self-organization of a robust metal–organic cluster based on copper(i) with chloride and organosulphur ligands

et al. 2015

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The design and fabrication of new nanostructures with controlled functionality, size, shape, and position are major goals in nanoscience. 1 The concept of self-assembly of molecular building blocks to generate well-defined architectures based on non-covalent interactions with the supporting substrate is technologically appealing. 2 Such intriguing supramolecular assemblies often possess polymeric characteristics and are referred to as ''supramolecular polymers''. 3 The generation of such organized structures, obtained by controlling supramolecular interactions, makes tuning of the physicochemical properties of these molecule based materials possible. In this context, to combine organic molecules with metal entities is particularly useful. 4,5 On the other hand, the bottom-up approach for forming on-surface nanostructures by direct sublimation of their building blocks under ultra-high vacuum conditions has been shown as an excellent approach to this goal. 6 However, this experimental approach presents a limitation coming from the stability that it is required for the molecule to allow sublimation without structural damage. This is the reason why there are a relatively high number of nanostructures based on organization of ideal organic molecules but few of them are based on the combination of organic molecules with metal fragments. 7 The metal-organic structures formed up to now by sublimation are almost limited to those simple cases obtained by sequential sublimation of both building blocks, organic molecules and metal precursors, or just by sublimation of the organic molecules and their subsequent in situ reaction with the metal atoms coming from the metallic surface. 8,9 In both cases the selection of the building blocks has allowed formation of a large variety of 1D-or 2D-coordination polymer architectures. [10][11][12] In most of the previous studies of large complex molecules on surfaces the molecules were transferred from a solution [13][14][15][16][17][18][19] or by a dry imprint technique 20 to the substrate in order to preserve the fragile core. In this communication we focus on the search of a new metal-organic complex with a robust structure able to be sublimated keeping its molecular integrity and to self-assemble without being disrupted by the surface. We have been able to directly sublimate under ultra-high vacuum (UHV) conditions a large metal-organic cluster that is, as far as we know, the largest molecular complex ever sublimated and in situ characterized by STM. This allows the formation of well-controlled nanoarchitectures readily on a surface and use of advanced surface in situ techniques. To achieve this goal, we combine in situ scanning tunnelling microscopy (STM), X-ray photoemission spectroscopy (XPS), and low energy electron diffraction (LEED) experiments with ab initio calculations.Recently, we have reported on the synthesis and characterization of a robust metal-organic cluster [Cu 4 (m 3 -Cl) 4 (m-pym 2 S 2 ) 4 ] (pym 2 S 2 = dipyrimidinedisulfide) (1) showing interesting physical and...

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Intermolecular Contrast in Atomic Force Microscopy Images without Intermolecular Bonds

Cited by 136 publications

References 28 publications

Calculating the Entropy Loss on Adsorption of Organic Molecules at Insulating Surfaces

Calculating the Entropy Loss on Adsorption of Organic Molecules at Insulating Surfaces

Simulating contrast inversion in atomic force microscopy imaging with real-space pseudopotentials

On-surface self-organization of a robust metal–organic cluster based on copper(i) with chloride and organosulphur ligands

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