Dynamics of porphyrin adsorption on highly oriented pyrolytic graphite monitored by scanning tunnelling microscopy at the liquid/solid interface

Ferreira, Quirina; Bragança, Ana M.; Moura, Nuno M. M.; Faustino, Maria A. F.; Alcácer, Luís; Morgado, Jorge

doi:10.1016/j.apsusc.2013.02.017

Cited by 12 publications

(23 citation statements)

References 33 publications

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“…In addition, peripheral protrusions around the molecule can be visible depending on the types of terminal groups that are linked to the macrocycle. In our case, the ethyl groups have high mobility and can adopt several molecular arrangements, depending on the inter‐ and intramolecular interactions (Ferreira et al ., ).…”

Section: Resultsmentioning

confidence: 97%

“…1B) with symmetrical peripheral substituents composed of two ethyl chains. The macrocyle core is stable under a wide range of temperatures, pH and other environmental conditions (Drain et al, 2009) but can suffer distortions and deformations (Shelnutt et al, 1998) including polymorphism during self-assembled monolayers formation (Ferreira et al, 2013).…”

Section: Resultsmentioning

confidence: 99%

“…These distortions also influence the conductivity of the porphyrins which is an important property for the design of organic electronic systems (Wolfle et al ., ; Ferreira et al . , , ). Recent publications have been reporting studies about the dynamic behaviour of porphyrins, in particular, conformational manipulations using STM (Zhao et al ., ; Kumagai et al ., ; Nandi et al ., ; Lensen et al ., ) and a recent review paper highlights some of the experiments that involved porphyrin manipulation using STM (Auwarter et al ., ).…”

Section: Introductionmentioning

confidence: 99%

“…For instance, the hemoproteins are an example of nonplanar porphryins that can adopt different molecular conformations controlling the activity of biological systems (Drain et al, 2009). These distortions also influence the conductivity of the porphyrins which is an important property for the design of organic electronic systems (Wolfle et al, 2008;Ferreira et al 2014Ferreira et al , 2011Ferreira et al , 2013. Recent publications have been reporting studies about the dynamic behaviour of porphyrins, in particular, conformational manipulations using STM (Zhao et al, 2013;Kumagai et al, 2014;Nandi et al, 2016;Lensen et al, 2012) and a recent review paper highlights some of the experiments that involved porphyrin manipulation using STM (Auwarter et al, 2015).…”

Section: Introductionmentioning

confidence: 99%

“…However, it is crucial to explore these molecular manipulations at room temperature. It is known that porphyrinic monolayers have high mobility leading to a high number of molecular arrangements that the molecules can adopt until achieving a thermodynamically stable conformation (Ferreira et al, 2013). It was observed, at the solid/liquid interface, that the porphyrins can switch between different polymorphs until achieving a stable monolayer.…”

Section: Introductionmentioning

confidence: 99%

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Sparse‐coding denoising applied to reversible conformational switching of a porphyrin self‐assembled monolayer induced by scanning tunnelling microscopy

Oliveira

Bragança

Alcácer

et al. 2018

Journal of Microscopy

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Scanning tunnelling microscopy (STM) was used to induce conformational molecular switching on a self-assembled monolayer of zinc-octaethylporphyrin on a graphite/tetradecane interface at room temperature. A reversible conformational change controlled by applying a tip voltage was observed. Consecutive STM images acquired at alternating tip voltages showed that at 0.4 V the porphyrin monolayer presents a molecular arrangement formed by alternate rows with two different types of structural conformations and when the potential is increased to 0.7 V the monolayer presents only one type of conformation. In this paper, we characterize these porphyrin conformational dynamics by analyzing the STM images, which were improved for better quality and interpretation by means of a denoising algorithm, adapted to process STM images from state of the art image processing and analysis methods. STM remains the best technique to 'see' and to manipulate the matter at atomic scale. A very sharp tip a few angstroms of the surface can provide images of molecules and atoms with a powerful resolution. However, these images are strongly affected by noise which is necessary to correct and eliminate. This paper is about new computational tools specifically developed to denoise the images acquired with STM. The new algorithms were tested in STM images, obtained at room temperature, of porphyrin monolayer which presents reversible conformational change in function of the tip bias voltage. Images with high resolution, acquired in real time, show that the porphyrins have different molecular arrangements whether the tip voltage is 0.4 V or 0.7 V.

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Section: Resultsmentioning

confidence: 97%