Browsing by Author "Spijker, Peter"

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  • Ab initio Kinetic Monte Carlo simulations of dissolution at the NaCl-water interface
    (2014) Chen, Jian-Cheng; Reischl, Bernhard; Spijker, Peter; Holmberg, Nico; Laasonen, Kari; Foster, Adam S.
     A1 Alkuperäisartikkeli tieteellisessä aikakauslehdessä
  • Atomic-resolution three-dimensional hydration structures on a heterogeneously charged surface
    (2017-12-01) Umeda, Kenichi; Zivanovic, Lidija; Kobayashi, Kei; Ritala, Juha; Kominami, Hiroaki; Spijker, Peter; Foster, Adam S.; Yamada, Hirofumi
     A1 Alkuperäisartikkeli tieteellisessä aikakauslehdessä
    Local hydration structures at the solid-liquid interface around boundary edges on heterostructures are key to an atomic-level understanding of various physical, chemical and biological processes. Recently, we succeeded in visualising atomic-scale three-dimensional hydration structures by using ultra-low noise frequency-modulation atomic force microscopy. However, the time-consuming three-dimensional-map measurements on uneven heterogeneous surfaces have not been achieved due to experimental difficulties, to the best of our knowledge. Here, we report the local hydration structures formed on a heterogeneously charged phyllosilicate surface using a recently established fast and nondestructive acquisition protocol. We discover intermediate regions formed at step edges of the charged surface. By combining with molecular dynamics simulations, we reveal that the distinct structural hydrations are hard to observe in these regions, unlike the charged surface regions, possibly due to the depletion of ions at the edges. Our methodology and findings could be crucial for the exploration of further functionalities.
  • Atomically controlled substitutional boron-doping of graphene nanoribbons
    (2015) Kawai, Shigeki; Saito, Shohei; Osumi, Shinichiro; Yamaguchi, Shigehiro; Foster, Adam S.; Spijker, Peter; Meyer, Ernst
     A1 Alkuperäisartikkeli tieteellisessä aikakauslehdessä
    Boron is a unique element in terms of electron deficiency and Lewis acidity. Incorporation of boron atoms into an aromatic carbon framework offers a wide variety of functionality. However, the intrinsic instability of organoboron compounds against moisture and oxygen has delayed the development. Here, we present boron-doped graphene nanoribbons (B-GNRs) of widths of N=7, 14 and 21 by on-surface chemical reactions with an employed organoboron precursor. The location of the boron dopant is well defined in the centre of the B-GNR, corresponding to 4.8 atom%, as programmed. The chemical reactivity of B-GNRs is probed by the adsorption of nitric oxide (NO), which is most effectively trapped by the boron sites, demonstrating the Lewis acid character. Structural properties and the chemical nature of the NO-reacted B-GNR are determined by a combination of scanning tunnelling microscopy, high-resolution atomic force microscopy with a CO tip, and density functional and classical computations.
  • Author Correction: Atomic-resolution three-dimensional hydration structures on a heterogeneously charged surface (Nature Communications DOI: 10.1038/s41467-017-01896-4)
    (2018-12-01) Umeda, Kenichi; Zivanovic, Lidija; Kobayashi, Kei; Ritala, Juha; Kominami, Hiroaki; Spijker, Peter; Foster, Adam S.; Yamada, Hirofumi
     Other contribution
    The original version of the Supplementary Information associated with this Article contained an error in Supplementary Figure 9e,f in which the y-axes were incorrectly labelled from '-40' to '40', rather than the correct '-400' to '400'. The HTML has been updated to include a corrected version of the Supplementary Information. Nature Communications, 2041-1723, Volume 9, Issue 1
  • 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
  • Hydration layers at the graphite-water interface: Attraction or confinement
    (2019-11-08) Soengen, Hagen; Jaques, Ygor Morais; Zivanovic, Lidija; Seibert, Sebastian; Bechstein, Ralf; Spijker, Peter; Onishi, Hiroshi; Foster, Adam S.; Kuehnle, Angelika
     A1 Alkuperäisartikkeli tieteellisessä aikakauslehdessä
    Water molecules at solid surfaces typically arrange in layers. The physical origin of the hydration layers is usually explained by two different reasons: (1) the attraction between the surface and water and (2) the water confinement due to the surface. While the attraction is specific to the particular solid, the confinement is a general property of surfaces; a differentiation between the two effects is, therefore, critical for research on interactions at aqueous interfaces. Here, we investigate the graphite-water interface, which is a widely used model system where the solid-water attraction is often considered to be negligible Similar to previous studies, we observe hydration layers using three-dimensional atomic force microscopy at the graphite-water interface. We explain why the confinement could cause the formation of hydration layers even in the absence of attraction between surface and water by employing Monte Carlo simulations. Using additional molecular dynamics simulations, we continue to show that at ambient conditions, however, the confinement alone does not cause the formation of layers at the graphite-water interface. We thereby demonstrate that there is a significant graphite-water attraction.
  • Mechanism of atomic force microscopy imaging of three-dimensional hydration structures at a solid-liquid interface
    (2015) Fukuma, Takeshi; Reischl, Bernhard; Kobayashi, Naritaka; Spijker, Peter; Federici Canova, Filippo; Miyazawa, Keisuke; Foster, Adam S.
     A1 Alkuperäisartikkeli tieteellisessä aikakauslehdessä
    Here we present both subnanometer imaging of three-dimensional (3D) hydration structures using atomic force microscopy (AFM) and molecular dynamics simulations of the calcite-water interface. In AFM, by scanning the 3D interfacial space in pure water and recording the force on the tip, a 3D force image can be produced, which can then be directly compared to the simulated 3D water density and forces on a model tip. Analyzing in depth the resemblance between experiment and simulation as a function of the tip-sample distance allowed us to clarify the contrast mechanism in the force images and the reason for their agreement with water density distributions. This work aims to form the theoretical basis for AFM imaging of hydration structures and enables its application to future studies on important interfacial processes at the molecular scale.
  • Molecular Resolution of the Water Interface at an Alkali Halide with Terraces and Steps
    (2016-09-08) Ito, Fumiaki; Kobayashi, Kei; Spijker, Peter; Zivanovic, Lidija; Umeda, Kenichi; Nurmi, Tarmo; Holmberg, Nico; Laasonen, Kari; Foster, Adam S.; Yamada, Hirofumi
     A2 Katsausartikkeli tieteellisessä aikakauslehdessä
    Hydration structures at crystal surfaces play important roles in crystal growth or dissolution processes in liquid environments. Recently developed two-dimensional (2D) and three-dimensional (3D) force mapping techniques using frequency-modulation atomic force microscopy (FM-AFM) allow us to visualize the hydration structures at the solid-liquid interfaces at angstrom-scale resolution in real space. Up to now, the experimental and theoretical studies on local hydration structures have mainly focused on those on the terrace, but little work has looked at step edges, usually the key areas in dissolution and growth. In this study, we measured local hydration structures on water-soluble alkali halide crystal surfaces by 2D force mapping FM-AFM. The atomic-scale hydration structures observed on the terraces agree well with molecular-dynamics (MD) simulations. We also measured the hydration structures at the step edge of the NaCl(001) surface, which was constantly dissolving and growing, leading to the clear observation of atomic fluctuations. We found, with the support of MD simulations, that the hydration structures measured by FM-AFM at a time scale of a minute can be interpreted as the time-average of the hydration structures on the upper terrace and those on the lower terrace.
  • Thermal control of sequential on-surface transformation of a hydrocarbon molecule on a copper surface
    (2016-09-13) Kawai, Shigeki; Haapasilta, Ville; Lindner, Benjamin D.; Tahara, Kazukuni; Spijker, Peter; Buitendijk, Jeroen A.; Pawlak, Rémy; Meier, Tobias; Tobe, Yoshito; Foster, Adam S.; Meyer, Ernst
     A1 Alkuperäisartikkeli tieteellisessä aikakauslehdessä
    On-surface chemical reactions hold the potential for manufacturing nanoscale structures directly onto surfaces by linking carbon atoms in a single-step reaction. To fabricate more complex and functionalized structures, the control of the on-surface chemical reactions must be developed significantly. Here, we present a thermally controlled sequential three-step chemical transformation of a hydrocarbon molecule on a Cu(111) surface. With a combination of high-resolution atomic force microscopy and first-principles computations, we investigate the transformation process in step-by-step detail from the initial structure to the final product via two intermediate states. The results demonstrate that surfaces can be used as catalysing templates to obtain compounds, which cannot easily be synthesized by solution chemistry.
  • 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.
  • Visualising the molecular alteration of the calcite (104) - Water interface by sodium nitrate
    (2016-02-15) Hofmann, Sascha; Voïtchovsky, Kislon; Spijker, Peter; Schmidt, Moritz; Stumpf, Thorsten
     A1 Alkuperäisartikkeli tieteellisessä aikakauslehdessä
    The reactivity of calcite, one of the most abundant minerals in the earth's crust, is determined by the molecular details of its interface with the contacting solution. Recently, it has been found that trace concentrations of NaNO3 severely affect calcite's (104) surface and its reactivity. Here we combine molecular dynamics (MD) simulations, X-ray reflectivity (XR) and in situ atomic force microscopy (AFM) to probe the calcite (104) - water interface in the presence of NaNO3. Simulations reveal density profiles of different ions near calcite's surface, with NO3 - able to reach closer to the surface than CO3 2- and in higher concentrations. Reflectivity measurements show a structural destabilisation of the (104) surfaces' topmost atomic layers in NaNO3 bearing solution, with distorted rotation angles of the carbonate groups and substantial displacement of the lattice ions. Nanoscale AFM results confirm the alteration of crystallographic characteristics, and the ability of dissolved NaNO3 to modify the structure of interfacial water was observed by AFM force spectroscopy. Our experiments and simulations consistently evidence a dramatic deterioration of the crystals' surface, with potentially important implications for geological and industrial processes.