Browsing by Author "Tracey, John"

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Competing Annulene and Radialene Structures in a Single Anti-Aromatic Molecule Studied by High-Resolution Atomic Force Microscopy
(2017-08-22) Kawai, Shigeki; Takahashi, Keisuke; Ito, Shingo; Pawlak, Rémy; Meier, Tobias; Spijker, Peter; Canova, Filippo Federici; Tracey, John; Nozaki, Kyoko; Foster, Adam S.; Meyer, Ernst
A1 Alkuperäisartikkeli tieteellisessä aikakauslehdessä
According to Hückel theory, an anti-aromatic molecule possessing (4n)π-electrons becomes unstable. Although the stabilization has been demonstrated by radialene-type structures - fusing aromatic rings to anti-aromatic rings - in solution, such molecules have never been studied at a single molecular level. Here, we synthesize a cyclobutadiene derivative, dibenzo[b,h]biphenylene, by an on-surface intramolecular reaction. With a combination of high-resolution atomic force microscopy and density functional theory calculations, we found that a radialene structure significantly reduces the anti-aromaticity of the cyclobutadiene core, extracting π-electrons, while the small four-membered cyclic structure keeps a high density of the total charge.
Direct quantitative measurement of the C=O center dot center dot center dot H-C bond by atomic force microscopy
(2017-05) Kawai, Shigeki; Nishiuchi, Tomohiko; Kodama, Takuya; Spijker, Peter; Pawlak, Remy; Meier, Tobias; Tracey, John; Kubo, Takashi; Meyer, Ernst; Foster, Adam S.
A1 Alkuperäisartikkeli tieteellisessä aikakauslehdessä
The hydrogen atom-the smallest and most abundant atom-is of utmost importance in physics and chemistry. Although many analysis methods have been applied to its study, direct observation of hydrogen atoms in a single molecule remains largely unexplored. We use atomic force microscopy (AFM) to resolve the outermost hydrogen atoms of propellane molecules via very weak C=O center dot center dot center dot H-C hydrogen bonding just before the onset of Pauli repulsion. The direct measurement of the interaction with a hydrogen atom paves the way for the identification of three-dimensional molecules such as DNAs and polymers, building the capabilities of AFMtoward quantitative probing of local chemical reactivity.
Dissolution Processes at Step Edges of Calcite in Water Investigated by High-Speed Frequency Modulation Atomic Force Microscopy and Simulation
(2017-07-12) Miyata, Kazuki; Tracey, John; Miyazawa, Keisuke; Haapasilta, Ville; Spijker, Peter; Kawagoe, Yuta; Foster, Adam S.; Tsukamoto, Katsuo; Fukuma, Takeshi
A1 Alkuperäisartikkeli tieteellisessä aikakauslehdessä
The microscopic understanding of the crystal growth and dissolution processes have been greatly advanced by the direct imaging of nanoscale step flows by atomic force microscopy (AFM), optical interferometry, and X-ray microscopy. However, one of the most fundamental events that govern their kinetics, namely, atomistic events at the step edges, have not been well understood. In this study, we have developed high-speed frequency modulation AFM (FM-AFM) and enabled true atomic-resolution imaging in liquid at ∼1 s/frame, which is ∼50 times faster than the conventional FM-AFM. With the developed AFM, we have directly imaged subnanometer-scale surface structures around the moving step edges of calcite during its dissolution in water. The obtained images reveal that the transition region with typical width of a few nanometers is formed along the step edges. Building upon insight in previous studies, our simulations suggest that the transition region is most likely to be a Ca(OH)2 monolayer formed as an intermediate state in the dissolution process. On the basis of this finding, we improve our understanding of the atomistic dissolution model of calcite in water. These results open up a wide range of future applications of the high-speed FM-AFM to the studies on various dynamic processes at solid-liquid interfaces with true atomic resolution.
Flexible and modular virtual scanning probe microscope
(2015) Tracey, John; Federici Canova, Filippo; Keisanen, Olli; Gao, David Z.; Spijker, Peter; Reischl, Bernhard; Foster, Adam S.
A1 Alkuperäisartikkeli tieteellisessä aikakauslehdessä
Multiple heteroatom substitution to graphene nanoribbon
(2018-04-13) Kawai, Shigeki; Nakatsuka, Soichiro; Hatakeyama, Takuji; Pawlak, Rémy; Meier, Tobias; Tracey, John; Meyer, Ernst; Foster, Adam S.
A1 Alkuperäisartikkeli tieteellisessä aikakauslehdessä
Substituting heteroatoms into nanostructured graphene elements, such as graphene nanoribbons, offers the possibility for atomic engineering of electronic properties. To characterize these substitutions, functionalized atomic force microscopy (AFM)-a tool to directly resolve chemical structures-is one of themost promising tools, yet the chemical analysis of heteroatoms has been rarely performed. We synthesized multiple heteroatom-substituted graphene nanoribbons and showed that AFM can directly resolve elemental differences and can be correlated to the van der Waals radii, as well as the modulated local electron density caused by the substitution. This elemental-sensitive measurement takes an important step in the analysis of functionalized two-dimensional carbon materials.
Simulating atomic force microscopy at the solid-liquid interface
(2017) Tracey, John
School of Science | Doctoral dissertation (article-based)
NC-AFM is an experimental technique that is capable of imaging, in principle, any surface at atomic resolution in any environment. Despite the clear advantages of NC-AFM, the biggest drawback is with regards to the interpretation of the results. Typically theoretical simulations are conducted to assist with this. A key component in linking theoretical simulations and the experimental results is the use of virtual machines. These aim to reproduce the experiment, allowing for a more complete simulation. The PyVAFM presented within, is such a virtual machine allowing users to reproduce any experimental setup or operational mode. It is fully open source, allowing future users to update the software with new cutting edge experimental components. Solid-liquid interfaces play a key role in many natural processes such as weathering or biomineralisation. In order to understand these processes, it is important to gain insight into the atomic structure behind them. Exploration of solid-liquid interfaces by NC-AFM is common, although due to the additional complexity of the environment as well as the experiment, the measured signal is difficult to relate to physical processes. As part of this work, we examine experimental results of Frequency Modulated-Atomic Force Microscopy (FM-AFM) on calcite in water and reproduce them using the PyVAFM, in an attempt to understand them in terms of average tip-sample distance. Building upon this we also considered steps on a calcite surface, studied using a new high speed AFM set-up. It was found that a shadow appeared at the step edge that was previously unseen. Using a combination of molecular dynamics and simulated AFM images we developed a model of the shadow region giving insight into the dissolution process. A chemically similar material to calcite, dolomite contains a similar crystal structure, but every second Ca is replaced with a Mg. Up until now identification of chemically alike species with the same surface charge has not been demonstrated in liquids and represents a new benchmark in sensitivity. By comparing the subtle differences in FM-AFM frequency shift curves as well as the simulated water densities above the various cations, it was possible for us to identify the Mg and Ca sites on dolomite. The main theme linking all these topics is in the analysis of NC-AFM images. From this it is clear that it still remains challenging and is typically done by eye. This is a very subjective approach and unscientific. In this final section we endeavour to produce an algorithm that uses Fourier analysis of images to produce a score of how similar the two images are. We produced an algorithm that is insensitive to phase, rotation, scale and resolution and designed specifically for comparison of NC-AFM images, allowing increased objectivity when making such comparisons.
Three-dimensional solvation structure of ethanol on carbonate minerals
(2020-06-10) Soengen, Hagen; Jaques, Ygor Morais; Spijker, Peter; Marutschke, Christoph; Klassen, Stefanie; Hermes, Ilka; Bechstein, Ralf; Zivanovic, Lidija; Tracey, John; Foster, Adam S.; Kuehnle, Angelika
A1 Alkuperäisartikkeli tieteellisessä aikakauslehdessä
Calcite and magnesite are important mineral constituents of the earth's crust. In aqueous environments, these carbonates typically expose their most stable cleavage plane, the (10.4) surface. It is known that these surfaces interact with a large variety of organic molecules, which can result in surface restructuring. This process is decisive for the formation of biominerals. With the development of 3D atomic force microscopy (AFM) it is now possible to image solid-liquid interfaces with unprecedented molecular resolution. However, the majority of 3D AFM studies have been focused on the arrangement of water at carbonate surfaces. Here, we present an analysis of the assembly of ethanol - an organic molecule with a single hydroxy group - at the calcite and magnesite (10.4) surfaces by using high-resolution 3D AFM and molecular dynamics (MD) simulations. Within a single AFM data set we are able to resolve both the first laterally ordered solvation layer of ethanol on the calcite surface as well as the following solvation layers that show no lateral order. Our experimental results are in excellent agreement with MD simulations. The qualitative difference in the lateral order can be understood by the differing chemical environment: While the first layer adopts specific binding positions on the ionic carbonate surface, the second layer resides on top of the organic ethyl layer. A comparison of calcite and magnesite reveals a qualitatively similar ethanol arrangement on both carbonates, indicating the general nature of this finding.
Tip dependence of three-dimensional scanning force microscopy images of calcite-water interfaces investigated by simulation and experiments
(2020-06-28) Miyazawa, Keisuke; Tracey, John; Reischl, Bernhard; Spijker, Peter; Foster, Adam S.; Rohl, Andrew L.; Fukuma, Takeshi
A1 Alkuperäisartikkeli tieteellisessä aikakauslehdessä
In this study, we have investigated the influence of the tip on the three-dimensional scanning force microscopy (3D-SFM) images of calcite-water interfaces by experiments and simulations. We calculated 3D force images by simulations with the solvent tip approximation (STA), Ca, CO3 and OH tip models. For all the 3D images, the z profiles at the surface Ca and CO3 sites alternately show oscillatory peaks corresponding to the hydration layers. However, the peak heights and spacings become larger when the mechanical stability of the tip becomes higher. For analyzing the xy slices of the 3D force images, we developed the extended STA (E-STA) model which allowed us to reveal the strong correlation between the hydration structure just under the tip and the atomic-scale force contrasts. Based on these understandings on the image features showing the strong tip dependence, we developed a method for objectively estimating the similarity between 3D force images. With this method, we compared the simulated images with the three experimentally obtained ones. Among them, two images showed a relatively high similarity with the image obtained by the simulation with the Ca or the CO3 tip model. Based on these agreements, we characterized the hydration structure and mechanical stability of the experimentally used tips. The understanding and methodology presented here should help us to derive accurate information on the tip and the interfacial structure from experimentally obtained 3D-SFM images.
Understanding 2D atomic resolution imaging of the calcite surface in water by frequency modulation atomic force microscopy
(2016-09-09) Tracey, John; Miyazawa, Keisuke; Spijker, Peter; Miyata, Kazuki; Reischl, Bernhard; Canova, Filippo Federici; Rohl, Andrew L.; Fukuma, Takeshi; Foster, Adam S.
A1 Alkuperäisartikkeli tieteellisessä aikakauslehdessä
Frequency modulation atomic force microscopy (FM-AFM) experiments were performed on the calcite (1014) surface in pure water, and a detailed analysis was made of the 2D images at a variety of frequency setpoints. We observed eight different contrast patterns that reproducibly appeared in different experiments and with different measurement parameters. We then performed systematic free energy calculations of the same system using atomistic molecular dynamics to obtain an effective force field for the tip-surface interaction. By using this force field in a virtual AFM simulation we found that each experimental contrast could be reproduced in our simulations by changing the setpoint, regardless of the experimental parameters. This approach offers a generic method for understanding the wide variety of contrast patterns seen on the calcite surface in water, and is generally applicable to AFM imaging in liquids.
Water Orientation at the Calcite-Water Interface
(2021-08-12) Söngen, Hagen; Schlegel, Simon J.; Morais Jaques, Ygor; Tracey, John; Hosseinpour, Saman; Hwang, Doyk; Bechstein, Ralf; Bonn, Mischa; Foster, Adam S.; Kühnle, Angelika; Backus, Ellen H.G.
A1 Alkuperäisartikkeli tieteellisessä aikakauslehdessä
Mineral-water interfaces play an important role in many natural as well as technological fields. Fundamental properties of these interfaces are governed by the presence of the interfacial water and its specific structure at the surface. Calcite is particularly interesting as a dominant rock-forming mineral in the earth's crust. Here, we combine atomic force microscopy, sum-frequency generation spectroscopy, and molecular dynamics simulations to determine the position and orientation of the water molecules in the hydration layers of the calcite surface with high resolution. While atomic force microscopy provides detailed information about the position of the water molecules at the interface, sum-frequency generation spectroscopy can deduce the orientation of the water molecules. Comparison of the calcite-water interface to the interfaces of magnesite-water, magnesite-ethanol, and calcite-ethanol reveals a comprehensive picture with opposite water orientations in the first and second layer of the interface, which is corroborated by the molecular dynamics simulations.