Publications by authors named "Spijker P"

Calcite dissolution is initiated by the formation of a nanoscale etch pit followed by step edge propagation and hence strongly influenced by the interactions between surface diffusing ions and step edges. However, such atomic-scale dynamics are mostly inaccessible with current imaging tools. Here, we overcome this limitation by using our recent development of high-speed frequency modulation atomic force microscopy.

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Article Synopsis
  • Calcite and magnesite are key minerals in the earth's crust that interact with organic molecules, influencing the formation of biominerals.
  • Advanced 3D atomic force microscopy (AFM) allows visualization of solid-liquid interfaces at a molecular level, focusing on how ethanol behaves on the surfaces of these carbonates.
  • The study shows that ethanol assembles in distinct layers on calcite and magnesite, with the first layer being well-ordered due to specific binding interactions, while subsequent layers are less ordered, reflecting the different chemical contexts.
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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.

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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.

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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.

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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.

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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.

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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⋅⋅⋅H-C hydrogen bonding just before the onset of Pauli repulsion.

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Solid-liquid interfaces are decisive for a wide range of natural and technological processes, including fields as diverse as geochemistry and environmental science as well as catalysis and corrosion protection. Dynamic atomic force microscopy nowadays provides unparalleled structural insights into solid-liquid interfaces, including the solvation structure above the surface. In contrast, chemical identification of individual interfacial atoms still remains a considerable challenge.

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We use dispersion-corrected density functional theory molecular dynamics simulations to predict the ionic, electronic and vibrational properties of the SrTiO/HO solid-liquid interface. Approximately 50% of surface oxygens on the planar SrO termination are hydroxylated at all studied levels of water coverage, the corresponding number being 15% for the planar TiO termination and 5% on the stepped TiO-terminated surface. The lateral ordering of the hydration structure is largely controlled by covalent-like surface cation to HO bonding and surface corrugation.

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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.

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Frequency modulation atomic force microscopy (FM-AFM) experiments were performed on the calcite (10[Formula: see text]4) 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.

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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.

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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.

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The influence of gas-surface interactions of a dilute gas confined between two parallel walls on the heat flux predictions is investigated using a combined Monte Carlo (MC) and molecular dynamics (MD) approach. The accommodation coefficients are computed from the temperature of incident and reflected molecules in molecular dynamics and used as effective coefficients in Maxwell-like boundary conditions in Monte Carlo simulations. Hydrophobic and hydrophilic wall interactions are studied, and the effect of the gas-surface interaction potential on the heat flux and other characteristic parameters like density and temperature is shown.

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We have used ab initio molecular dynamics (AIMD) simulations to study the interaction of water with the NaCl surface. As expected, we find that water forms several ordered hydration layers, with the first hydration layer having water molecules aligned so that oxygen atoms are on average situated above Na sites. In an attempt to understand the dissolution of NaCl in water, we have then combined AIMD with constrained barrier searches, to calculate the dissolution energetics of Na(+) and Cl(-) ions from terraces, steps, corners and kinks of the (100) surface.

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When immersed into water, most solids develop a surface charge, which is neutralized by an accumulation of dissolved counterions at the interface. Although the density distribution of counterions perpendicular to the interface obeys well-established theories, little is known about counterions' lateral organization at the surface of the solid. Here we show, by using atomic force microscopy and computer simulations, that single hydrated metal ions can spontaneously form ordered structures at the surface of homogeneous solids in aqueous solutions.

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Calcite is among the most abundant minerals on earth and plays a central role in many environmental and geochemical processes. Here we used amplitude modulation atomic force microscopy (AFM) operated in a particular regime to visualize single ions close to the (1014) surface of calcite in solution. The results were acquired at equilibrium, in aqueous solution containing different concentrations of NaCl, RbCl, and CaCl(2).

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Many biological cellular processes occur at the micro- or millisecond time scale. With traditional all-atom molecular modeling techniques it is difficult to investigate the dynamics of long time scales or large systems, such as protein aggregation or activation. Coarse graining (CG) can be used to reduce the number of degrees of freedom in such a system, and reduce the computational complexity.

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For understanding the behavior of a gas close to a channel wall it is important to model the gas-wall interactions as detailed as possible. When using molecular dynamics simulations these interactions can be modeled explicitly, but the computations are time consuming. Replacing the explicit wall with a wall model reduces the computational time but the same characteristics should still remain.

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A variety of factors, including changes in temperature or osmotic pressure, can trigger morphological transitions of vesicles. Upon osmotic upshift, water diffuses across the membrane in response to the osmotic difference, resulting in a decreased vesicle volume to membrane area ratio and, consequently, a different shape. In this paper, we study the vesicle deformations on osmotic deflation using coarse grained molecular dynamics simulations.

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Self-assembled bilayer membranes have a remarkable inclination to form closed shells or vesicles. This bilayer-vesicle transition has been shown experimentally and by various kinds of computer simulation techniques. Here we study this transition using coarse-grained molecular dynamics.

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Recently we predicted the 3D structure of the human beta2-adrenergic receptor (beta2AR) and of the binding site of several agonists and antagonists to beta2AR. These predictions (MembStruk and HierDock) included no explicit water and only a few lipid molecules. Here we include explicit H(2)O and an infinite lipid bilayer membrane in molecular dynamics (MD) simulations of three systems: apo-beta2AR, epinephrine-bound beta2AR, and butoxamine-bound beta2AR (epinephrine is an endogenous agonist, and butoxamine is a beta2AR selective antagonist).

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