Free Energy Approaches for Modeling Atomic Force Microscopy in Liquids

Revealing the Mechanism Underlying 3D-AFM Imaging of Suspended Structures by Experiments and Simulations

The invention of 3D atomic force microscopy (3D-AFM) has enabled visualizing subnanoscale 3D hydration structures. Meanwhile, its applications to imaging flexible molecular chains have started to be experimentally explored. However, the validity and principle of such imaging have yet to be clarified by comparing experiments and simulations or cross-observations with an alternative technique. Such studies are impeded by the lack of an appropriate model. Here, this difficulty is overcome by fabricating 3D carbon nanotube (CNT) structures flexible enough for 3D-AFM, large enough for scanning electron microscopy (SEM), and simple enough for simulations. SEM and 3D-AFM observations of the same model provide unambiguous evidence to support the possibility of imaging overlapped nanostructures, such as suspended CNT and underlying platinum (Pt) nanodots. Langevin dynamics simulations of such 3D-AFM imaging clarify the imaging mechanism, where the flexible CNT is laterally displaced to allow the AFM probe access to the underlying structures. These results consistently show that 3D-AFM images are affected by the friction between the CNT and AFM nanoprobe, yet it can be significantly suppressed by oscillating the cantilever. This study reinforces the theoretical basis of 3D-AFM for imaging various 3D self-organizing systems in diverse fields, from life sciences to interface sciences.

Computation of topographic and three-dimensional atomic force microscopy images of biopolymers by calculating forces

Atomic force microscopy (AFM) is widely utilized to visualize the molecular motions of biomolecules. Comparison of experimentally measured AFM images with simulated AFM images based on known structures of biomolecules is often necessary to elucidate what is actually resolved in the images. Experimental AFM images are generated by force measurements; however, conventional AFM simulation has been based on geometrical considerations rather than calculating forces using molecular dynamics simulations due to limited computation time. This letter summarizes recently developed methods to simulate topographic and three-dimensional AFM (3D-AFM) images of biopolymers such as chromosomes and cytoskeleton fibers. Scanning such biomolecules in AFM measurements usually results in nonequilibrium-type work being performed. As such, the Jarzynski equality was employed to relate the nonequilibrium work to the free energy profiles, and the forces were calculated by differentiating the free energy profiles. The biomolecules and probes were approximated using a supra-coarse-grained model, allowing the simulation of force-distance curves in feasible time. It was found that there is an optimum scanning velocity and that some of polymer structures are resolved in the simulated 3D-AFM images. The theoretical background adopted to rationalize the use of small probe radius in the conventional AFM simulation of biomolecules is clarified.

Ion adsorption and hydration forces: a comparison of crystalline mica vs. amorphous silica surfaces

Hydration forces are ubiquitous in nature and technology. Yet, the characterization of interfacial hydration structures and their dependence on the nature of the substrate and the presence of ions have remained challenging and controversial. We present a systematic study using dynamic Atomic Force Microscopy of hydration forces on mica surfaces and amorphous silica surfaces in aqueous electrolytes containing chloride salts of various alkali and earth alkaline cations of variable concentrations at pH values between 3 and 9. Our measurements with ultra-sharp AFM tips demonstrate the presence of both oscillatory and monotonically decaying hydration forces of very similar strength on both atomically smooth mica and amorphous silica surfaces with a roughness comparable to the size of a water molecule. The characteristic range of the forces is approximately 1 nm, independent of the fluid composition. Force oscillations are consistent with the size of water molecules for all conditions investigated. Weakly hydrated Cs+ ions are the only exception: they disrupt the oscillatory hydration structure and induce attractive monotonic hydration forces. On silica, force oscillations are also smeared out if the size of the AFM tip exceeds the characteristic lateral scale of the surface roughness. The observation of attractive monotonic hydration forces for asymmetric systems suggests opportunities to probe water polarization.

Three-dimensional ordering of water molecules reflecting hydroxyl groups on sapphire (001) and α-quartz (100) surfaces

Water molecules on oxide surfaces influence the chemical reactivity and molecular adsorption behavior of oxides. Herein, three-dimensional atomic force microscopy (3D-AFM) and molecular dynamics simulations are used to visualize the surface hydroxyl (OH) groups and their hydration structures on sapphire (001) and α-quartz (100) surfaces at the atomic-scale. The obtained results revealed that the spatial density distributions and hydrogen-bonding strengths of surface OH groups affect their local hydration structures. In particular, the force curves obtained by 3D-AFM suggest that the hydration forces of water molecules intensify at sites where water molecules strongly interact with the surface OH groups. The insights obtained in this study deepen our understanding of the affinities of Al2O3 and SiO2 for water molecules and contribute to the use of 3D-AFM in the investigation of atomic-scale hydration structures on various surfaces, thereby benefiting a wide range of research fields dealing with solid-liquid interfaces.

Simulations of Subnanometer Scale Image Contrast in Atomic Force Microscopy of Self-Assembled Monolayers in Water

Achieving high-resolution images using dynamic atomic force microscopy (AFM) requires understanding how chemical and structural features of the surface affect image contrast. This understanding is particularly challenging when imaging samples in water. An initial step is to determine how well-characterized surface features interact with the AFM tip in wet environments. Here, we use molecular dynamics simulations of a model AFM tip apex oscillating in water above self-assembled monolayers (SAMs) with different chain lengths and functional groups. The amplitude response of the tip is characterized across a range of vertical distances and amplitude set points. Then relative image contrast is quantified as the difference of the amplitude response of the tip when it is positioned directly above a SAM functional group vs positioned between two functional groups. Differences in contrast between SAMs with different lengths and functional groups are explained in terms of the vertical deflection of the SAMs due to interactions with the tip and water during dynamic imaging. The knowledge gained from simulations of these simple model systems may ultimately be used to guide selection of imaging parameters for more complex surfaces.

Interfacial Liquid Water on Graphite, Graphene, and 2D Materials

The optical, electronic, and mechanical properties of graphite, few-layer, and two-dimensional (2D) materials have prompted a considerable number of applications. Biosensing, energy storage, and water desalination illustrate applications that require a molecular-scale understanding of the interfacial water structure on 2D materials. This review introduces the most recent experimental and theoretical advances on the structure of interfacial liquid water on graphite-like and 2D materials surfaces. On pristine conditions, atomic-scale resolution experiments revealed the existence of 1-3 hydration layers. Those layers were separated by ∼0.3 nm. The experimental data were supported by molecular dynamics simulations. However, under standard working conditions, atomic-scale resolution experiments revealed the presence of 2-3 hydrocarbon layers. Those layers were separated by ∼0.5 nm. Linear alkanes were the dominant molecular specie within the hydrocarbon layers. Paradoxically, the interface of an aged 2D material surface immersed in water does not have water molecules on its vicinity. Free-energy considerations favored the replacement of water by alkanes.

How lignin sticks to cellulose-insights from atomic force microscopy enhanced by machine-learning analysis and molecular dynamics simulations

Elucidating cellulose-lignin interactions at the molecular and nanometric scales is an important research topic with impacts on several pathways of biomass valorization. Here, the interaction forces between a cellulosic substrate and lignin are investigated. Atomic force microscopy with lignin-coated tips is employed to probe the site-specific adhesion to a cellulose film in liquid water. Over seven thousand force-curves are analyzed by a machine-learning approach to cluster the experimental data into types of cellulose-tip interactions. The molecular mechanisms for distinct types of cellulose-lignin interactions are revealed by molecular dynamics simulations of lignin globules interacting with different cellulose Iβ crystal facets. This unique combination of experimental force-curves, data-driven analysis, and molecular simulations opens a new approach of investigation and updates the understanding of cellulose-lignin interactions at the nanoscale.

Computed Three-Dimensional Atomic Force Microscopy Images of Biopolymers Using the Jarzynski Equality

Three-dimensional atomic force microscopy (3D-AFM) has resolved three-dimensional distributions of solvent molecules at solid-liquid interfaces at the subnanometer scale. This method is now being extended to the imaging of biopolymer assemblies such as chromosomes or proteins in cells, with the expectation of being able to resolve their three-dimensional structures. Here, we have developed a computational method to simulate 3D-AFM images of biopolymers by using the Jarzynski equality. It is found that some parts of the fiber structure of biopolymers are indeed resolved in the 3D-AFM image. The dependency of 3D-AFM images on the vertical scanning velocity is investigated, and optimum scanning velocities are found. It is also clarified that forces in nonequilibrium processes are measured in 3D-AFM measurements when the dynamics of polymers are slower than the scanning of the probe.

Structured Water Molecules on Membrane Proteins Resolved by Atomic Force Microscopy

Water structuring on the outer surface of protein molecules called the hydration shell is essential as well as the internal water structures for higher-order structuring of protein molecules and their biological activities in vivo. We now show the molecular-scale hydration structure measurements of native purple membrane patches composed of proton pump proteins by a noninvasive three-dimensional force mapping technique based on frequency modulation atomic force microscopy. We successfully resolved the ordered water molecules localized near the proton uptake channels on the cytoplasmic side of the individual bacteriorhodopsin proteins in the purple membrane. We demonstrate that the three-dimensional force mapping can be widely applicable for molecular-scale investigations of the solid-liquid interfaces of various soft nanomaterials.

High-Speed Atomic Force Microscopy of the Structure and Dynamics of Calcite Nanoscale Etch Pits

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. By visualizing atomic-scale structural changes of the etch pits at the calcite surface in water, we found the existence of mobile and less-mobile surface adsorption layers (SALs) in the etch pits. We also found that some etch pits maintain their size for a long time without expansion, and their step edges are often associated with less-mobile SALs, suggesting their step stabilization effect.

Reducing molecular simulation time for AFM images based on super-resolution methods

Atomic force microscopy (AFM) has been an important tool for nanoscale imaging and characterization with atomic and subatomic resolution. Theoretical investigations are getting highly important for the interpretation of AFM images. Researchers have used molecular simulation to examine the AFM imaging mechanism. With a recent flurry of researches applying machine learning to AFM, AFM images obtained from molecular simulation have also been used as training data. However, the simulation is incredibly time consuming. In this paper, we apply super-resolution methods, including compressed sensing and deep learning methods, to reconstruct simulated images and to reduce simulation time. Several molecular simulation energy maps under different conditions are presented to demonstrate the performance of reconstruction algorithms. Through the analysis of reconstructed results, we find that both presented algorithms could complete the reconstruction with good quality and greatly reduce simulation time. Moreover, the super-resolution methods can be used to speed up the generation of training data and vary simulation resolution for AFM machine learning.

Predicting hydration layers on surfaces using deep learning

Characterisation of the nanoscale interface formed between minerals and water is essential to the understanding of natural processes, such as biomineralization, and to develop new technologies where function is dominated by the mineral-water interface. Atomic force microscopy offers the potential to characterize solid-liquid interfaces in high-resolution, with several experimental and theoretical studies offering molecular scale resolution by linking measurements directly to water density on the surface. However, the theoretical techniques used to interpret such results are computationally intensive and development of the approach has been limited by interpretation challenges. In this work, we develop a deep learning architecture to learn the solid-liquid interface of polymorphs of calcium carbonate, allowing for the rapid predictions of density profiles with reasonable accuracy.

First Steps towards Understanding the Non-Linear Impact of Mg on Calcite Solubility: A Molecular Dynamics Study

Magnesium (Mg2+) is one of the most common impurities in calcite and is known to have a non-linear impact on the solubility of magnesian calcites. Using molecular dynamics (MD), we observed that Mg2+ impacts overall surface energies, local free energy profiles, interfacial water density, structure and dynamics and, at higher concentrations, it also causes crystal surface deformation. Low Mg concentrations did not alter the overall crystal structure, but stabilised Ca2+ locally and tended to increase the etch pit nucleation energy. As a result, Ca-extraction energies over a wide range of 39 kJ/mol were observed. Calcite surfaces with an island were less stable compared to flat surfaces, and the incorporation of Mg2+ destabilised the island surface further, increasing the surface energy and the calcium extraction energies. In general, Ca2+ is less stable in islands of high Mg2+ concentrations. The local variation in free energies depends on the amount and distance to nearest Mg in addition to local disruption of interfacial water and the flexibility of surface carbonate ions to rotate. The result is a complex interplay of these characteristics that cause variability in local dissolution energies. Taken together, these results illustrate molecular scale processes behind the non-linear impact of Mg2+ concentration on the solubility of magnesium-bearing calcites.

Practical Guide to Single-Protein AFM Nanomechanical Spectroscopy Mapping: Insights and Pitfalls As Unraveled by All-Atom MD Simulations on Immunoglobulin G

Atomic force microscopy is an invaluable characterization tool in almost every biophysics laboratory. However, obtaining atomic/sub-nanometer resolution on single proteins has thus far remained elusive-a feat long achieved on hard substrates. In this regard, nanomechanical spectroscopy mapping may provide a viable approach to overcome this limitation. By complementing topography with mechanical properties measured locally, one may thus enhance spatial resolution at the single-protein level. In this work, we perform all-atom molecular dynamics simulations of the indentation process on a single immunoglobulin G (IgG) adsorbed on a graphene slab. Our simulations reveal three different stages as a function of strain: a noncontact regime-where the mechanical response is linked to the presence of the water environment- followed by an elastic response and a final plastic deformation regime. In the noncontact regime, we are able to identify hydrophobic/hydrophilic patches over the protein. This regime provides the most local mechanical information that allows one to discern different regions with similar height/topography and leads to the best spatial resolution. In the elastic regime, we conclude that the Young modulus is a well-defined property only within mechanically decoupled domains. This is caused by the fact that the elastic deformation is associated with a global reorganization of the domain. Differences in the mechanical response are large enough to clearly resolve domains within a single protein, such as the three subunits forming the IgG. Two events, unfolding or protein slipping, are observed in the plastic regime. Our simulations allow us to characterize these two processes and to provide a strategy to identify them in the force curves. Finally, we elaborate on possible challenges that could hamper the interpretation of such experiments/simulations and how to overcome them. All in all, our simulations provide a detailed picture of nanomechanical spectroscopy mapping on single proteins, showing its potential and the challenges that need to be overcome to unlock its full potential.

Subnanometer-scale imaging of nanobio-interfaces by frequency modulation atomic force microscopy

Recently, there have been significant advancements in dynamic-mode atomic force microscopy (AFM) for biological applications. With frequency modulation AFM (FM-AFM), subnanometer-scale surface structures of biomolecules such as secondary structures of proteins, phosphate groups of DNAs, and lipid-ion complexes have been directly visualized. In addition, three-dimensional AFM (3D-AFM) has been developed by combining a high-resolution AFM technique with a 3D tip scanning method. This method enabled visualization of 3D distributions of water (i.e. hydration structures) with subnanometer-scale resolution on various biological molecules such as lipids, proteins, and DNAs. Furthermore, 3D-AFM also allows visualization of subnanometer-scale 3D distributions of flexible surface structures such as thermally fluctuating lipid headgroups. Such a direct local information at nano-bio interfaces can play a critical role in determining the atomic- or molecular-scale model to explain interfacial structures and functions. Here, we present an overview of these recent advancements in the dynamic-mode AFM techniques and their biological applications.

Nanomechanical mapping of soft materials with the atomic force microscope: methods, theory and applications

Fast, high-resolution, non-destructive and quantitative characterization methods are needed to develop materials with tailored properties at the nanoscale or to understand the relationship between mechanical properties and cell physiology. This review introduces the state-of-the-art force microscope-based methods to map at high-spatial resolution the elastic and viscoelastic properties of soft materials. The experimental methods are explained in terms of the theories that enable the transformation of observables into material properties. Several applications in materials science, molecular biology and mechanobiology illustrate the scope, impact and potential of nanomechanical mapping methods.

Tip dependence of three-dimensional scanning force microscopy images of calcite-water interfaces investigated by simulation and experiments

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.

Atomic Force Microscopy Imaging of Crystalline Sucrose in Alcohols

Imaging nanometer- or molecule-scale topography has been achieved by dynamic atomic force microscopy (AFM) when a solid object of interest is damaged by vacuum exposure or electron irradiation. Imaging in a liquid offers a means to remove contaminations from the surface scanned using the microscope tip when the object is soluble to the surrounding liquid, typically water. In the present study, we attempted to take topographic images of crystalline sucrose. A problem arose due to the high solubility of this compound to water. Cantilever oscillation could not be excited in the saturated, viscous aqueous solution. By using n-hexanol instead of water, the solubility in the solvent and thus viscosity of the solution were reduced sufficiently to excite cantilever oscillation. Single-height steps and sucrose molecules were recognized in the images and thereby recorded on the (001)-oriented facets of sucrose crystals. Furthermore, two-dimensional distribution of liquid-induced force pushing or pulling the tip was mapped on planes perpendicular to the hexanol-sucrose interface. Observed uneven force distributions indicated liquid hexanol structured on the corrugated surface of sucrose. The viscosity tuning demonstrated here, which is not limited to hexanol instead of water, extends the range of liquid-solid interfaces to be probed by dynamic AFM.

Nanometer-Scale Distribution of a Lubricant Modifier on Iron Films: A Frequency-Modulation Atomic Force Microscopy Study Combined with a Friction Test

Liquid lubricants used in mechanical applications are low-vapor-pressure hydrocarbons modified with a small quantity of polar compounds. The polar modifiers adsorbed on the surface of sliding solids dominate the friction properties when the sliding surfaces are in close proximity. However, a few methods are available for the characterization of the adsorbed modifiers of a nanometer-scale thickness. In this study, we applied frequency-modulation atomic force microscopy to evaluate the vertical and lateral density distributions of the adsorbed modifier in a real lubricant, namely, poly-α-olefin (PAO) modified with an orthophosphoric acid oleyl ester. The liquid-induced force on the probing tip was mapped on a plane that was perpendicular to the lubricant-iron interface with a force sensitivity on the order of 10 pN. The PAO in the absence of the ester modifier was directly exposed to the film, which produced a few liquid layers parallel to the film surface with layer-to-layer distances of 0.6-0.7 nm. A monomolecular layer of the modifier was intermittently adsorbed with increasing ester concentration in the bulk lubricant, with complete coverage seen at 20 ppm. The C₁₈H₃₅ chains of the oleyl esters fluctuating in the lubricant produced a repulsive force on the tip, which monotonically decayed with the tip-to-surface distance. The dynamic friction coefficient of sliding steel-lubricant-steel interfaces, which was separately determined using a friction tester, was compared with the force map determined on the iron film immersed in the corresponding lubricant. The complete monomolecular layer of the ester modifier on the static lubricant-iron boundary is a requirement for achieving smooth and stable friction at the sliding interface.

Advances in Atomic Force Microscopy: Weakly Perturbative Imaging of the Interfacial Water

The structure and dynamics of interfacial water, determined by the water-interface interactions, are important for a wide range of applied fields and natural processes, such as water diffusion (Kim et al., 2013), electrochemistry (Markovic, 2013), heterogeneous catalysis (Over et al., 2000), and lubrication (Zilibotti et al., 2013). The precise understanding of water-interface interactions largely relies on the development of atomic-scale experimental techniques (Guo et al., 2014) and computational methods (Hapala et al., 2014b). Scanning probe microscopy has been extensively applied to probe interfacial water in many interdisciplinary fields (Ichii et al., 2012; Shiotari and Sugimoto, 2017; Peng et al., 2018a). In this perspective, we review the recent progress in the noncontact atomic force microscopy (nc-AFM) imaging and AFM simulation techniques and discuss how the newly developed techniques are applied to study the properties of interfacial water. The nc-AFM with the quadrupole-like CO-terminated tip can achieve ultrahigh-resolution imaging of the interfacial water on different surfaces, trace the reconstruction of H-bonding network and determine the intrinsic structures of the weakly bonded water clusters and even their metastable states. In the end, we present an outlook on the directions of future AFM studies of interfacial water as well as the challenges faced by this field.

Ion-Specific and pH-Dependent Hydration of Mica-Electrolyte Interfaces

Hydration forces play a crucial role in a wide range of phenomena in physics, chemistry, and biology. Here, we study the hydration of mica surfaces in contact with various alkali chloride solutions over a wide range of concentrations and pH values. Using atomic force microscopy and molecular dynamics simulations, we demonstrate that hydration forces consist of a superposition of a monotonically decaying and an oscillatory part, each with a unique dependence on the specific type of cation. The monotonic hydration force gradually decreases in strength with decreasing bulk hydration energy, leading to a transition from an overall repulsive (Li+, Na+) to an attractive (Rb+, Cs+) force. The oscillatory part, in contrast, displays a binary character, being hardly affected by the presence of strongly hydrated cations (Li+, Na+), but it becomes completely suppressed in the presence of weakly hydrated cations (Rb+, Cs+), in agreement with a less pronounced water structure in simulations. For both aspects, K+ plays an intermediate role, and decreasing pH follows the trend of increasing Rb+ and Cs+ concentrations.

Atomic- and Molecular-Resolution Mapping of Solid-Liquid Interfaces by 3D Atomic Force Microscopy

Hydration layers are ubiquitous in life and technology. Hence, interfacial aqueous layers have a central role in a wide range of phenomena from materials science to molecular and cell biology. A complete understanding of those processes requires, among other things, the development of very-sensitive and high-resolution instruments. Three-dimensional atomic force microscopy (3D-AFM) represents the latest and most successful attempt to generate atomically resolved three-dimensional images of solid-liquid interfaces. This review provides an overview of the 3D-AFM operating principles and its underlying physics. We illustrate and explain the capability of the instrument to resolve atomic defects on crystalline surfaces immersed in liquid. We also illustrate some of its applications to imaging the hydration structures on DNA or proteins. In the last section, we discuss some perspectives on emerging applications in materials science and molecular biology.

Molecular features of hydration layers probed by atomic force microscopy

Structurally-ordered layers of water are universally formed on a solid surface in aqueous solution or under ambient conditions. Although such hydration layers are commonly probed via atomic force microscopy (AFM), the current understanding on how the hydration layers manifest themselves in an AFM experiment is far from complete. By using molecular dynamics simulation, we investigate the hydration layers on a hydrophilic or hydrophobic surface probed by a nanoscale tip. We study the density and molecular orientation of water, the free energy, and the force on the tip by varying the tip-surface distance. The force-distance curve oscillates due to the transition between the mono-, bi-, and tri-layers of water confined between the tip and the surface. If both the tip and the surface are hydrophobic, water confined between the tip and the surface evaporates due to the dewetting transition, giving a hydrophobic force without oscillation. The periodicity of oscillation in the force differs from the structural periodicity of water. With a close proximity of the tip, the molecular dipoles align parallel to the surface, regardless of whether the tip and the surface are hydrophilic or hydrophobic.

Combined Experimental and Simulation Study of Amplitude Modulation Atomic Force Microscopy Measurements of Self-Assembled Monolayers in Water

Atomic force microscopy (AFM) can be used to measure surface properties at the nanoscale. However, interpretation of measurements from amplitude modulation AFM (AM-AFM) in liquid is not straightforward due to the interactions between the AFM tip, the surface being imaged, and the water. In this work, amplitude-distance measurements and molecular dynamics simulations of AM-AFM were employed to study the effect of surface chemistry on the amplitude of tip oscillation in water. The sample surfaces consisted of self-assembled monolayers where the hydrophilicity or hydrophobicity was determined by the terminal group of the alkanethiols. Analysis showed that surface chemical composition influences the hydration structure near the interface which affects the forces experienced by the tip and in turn changes the amplitude profile. This observation could aid our understanding of AM-AFM measurements of interfacial phenomena on various surfaces in water.

Resolving Point Defects in the Hydration Structure of Calcite (10.4) with Three-Dimensional Atomic Force Microscopy

It seems natural to assume that defects at mineral surfaces critically influence interfacial processes such as the dissolution and growth of minerals in water. The experimental verification of this claim, however, is challenging and requires real-space methods with utmost spatial resolution, such as atomic force microscopy (AFM). While defects at mineral-water interfaces have been resolved in 2D AFM images before, the perturbation of the surrounding hydration structure has not yet been analyzed experimentally. In this Letter, we demonstrate that point defects on the most stable and naturally abundant calcite (10.4) surface can be resolved using high-resolution 3D AFM-even within the fifth hydration layer. Our analysis of the hydration structure surrounding the point defect shows a perturbation of the hydration with a lateral extent of approximately one unit cell. These experimental results are corroborated by molecular dynamics simulations.

Electroviscous Dissipation in Aqueous Electrolyte Films with Overlapping Electric Double Layers

We use dynamic atomic force microscopy (AFM) to investigate the forces involved in squeezing out thin films of aqueous electrolyte between an AFM tip and silica substrates at variable pH and salt concentration. From amplitude and phase of the AFM signal we determine both conservative and dissipative components of the tip sample interaction forces. The measured dissipation is enhanced by up to a factor of 5 at tip-sample separations of ≈ one Debye length compared to the expectations based on classical hydrodynamic Reynolds damping with bulk viscosity. Calculating the surface charge density from the conservative forces using Derjaguin-Landau-Verwey-Overbeek (DLVO) theory in combination with a charge regulation boundary condition we find that the viscosity enhancement correlates with increasing surface charge density. We compare the observed viscosity enhancement with two competing continuum theory models: (i) electroviscous dissipation due to the electrophoretic flow driven by the streaming current that is generated upon squeezing out the counterions in the diffuse part of the electric double layer, and (ii) visco-electric enhancement of the local water viscosity caused by the strong electric fields within the electric double layer. While the visco-electric model correctly captures the qualitative trends observed in the experiments, a quantitative description of the data presumably requires more sophisticated simulations that include microscopic aspects of the distribution and mobility of ions in the Stern layer.

Atomic-resolution three-dimensional hydration structures on a heterogeneously charged surface

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.

Local hydration structures at solid-liquid interfaces are important in catalytic, electrochemical, and biological processes. Here, the authors demonstrate atomic-scale 3D hydration structures around the boundary on a heterogeneous mineral surface using atomic force microscopy experiments and molecular dynamics simulations.

Charge Induced Dynamics of Water in a Graphene-Mica Slit Pore

We use atomic force microscopy to in situ investigate the dynamic behavior of confined water at the interface between graphene and mica. The graphene is either uncharged, negatively charged, or positively charged. At high humidity, a third water layer will intercalate between graphene and mica. When graphene is negatively charged, the interface fills faster with a complete three layer water film, compared to uncharged graphene. As charged positively, the third water layer dewets the interface, either by evaporation into the ambient or by the formation of three-dimensional droplets under the graphene, on top of the bilayer. Our experimental findings reveal novel phenomena of water at the nanoscale, which are interesting from a fundamental point of view and demonstrate the direct control over the wetting properties of the graphene/water interface.

Influence of ions on two-dimensional and three-dimensional atomic force microscopy at fluorite-water interfaces

Recent advancement in liquid-environment atomic force microscopy (AFM) has enabled us to visualize three-dimensional (3D) hydration structures as well as two-dimensional (2D) surface structures with subnanometer-scale resolution at solid-water interfaces. However, the influence of ions present in solution on the 2D- and 3D-AFM measurements has not been well understood. In this study, we perform atomic-scale 2D- and 3D-AFM measurements at fluorite-water interfaces in pure water and a supersaturated solution of fluorite. The images obtained in these two environments are compared to understand the influence of the ions in solution on these measurements. In the 2D images, we found clear difference in the nanoscale structures but no significant difference in the atomic-scale contrasts. However, the 3D force images show clear difference in the subnanometer-scale contrasts. The force contrasts measured in pure water largely agree with those expected from the molecular dynamics simulation and the solvent tip approximation model. In the supersaturated solution, an additional force peak is observed over the negatively charged fluorine ion site. This location suggests that the observed force peak may originate from cations adsorbed on the fluorite surface. These results demonstrate that the ions can significantly alter the subnanometer-scale force contrasts in the 3D-AFM images.

Direct observation of the dynamics of single metal ions at the interface with solids in aqueous solutions

The dynamics of ions adsorbed at the surface of immersed charged solids plays a central role in countless natural and industrial processes such as crystal growth, heterogeneous catalysis, electrochemistry, or biological function. Electrokinetic measurements typically distinguish between a so-called Stern layer of ions and water molecules directly adsorbed on to the solid’s surface, and a diffuse layer of ions further away from the surface. Dynamics within the Stern layer remain poorly understood, largely owing to a lack of in-situ atomic-level insights. Here we follow the dynamics of single Rb⁺ and H₃O⁺ ions at the surface of mica in water using high-resolution atomic force microscopy with 25 ms resolution. Our results suggest that single hydrated Rb⁺ions reside τ₁ = 104 ± 5 ms at a given location, but this is dependent on the hydration state of the surface which evolves on a slower timescale of τ₂ = 610 ± 30 ms depending on H₃O⁺ adsorption. Increasing the liquid’s temperature from 5 °C to 65 °C predictably decreases the apparent glassiness of the interfacial water, but no clear effect on the ions’ dynamics was observed, indicating a diffusion-dominated process. These timescales are remarkably slow for individual monovalent ions and could have important implications for interfacial processes in electrolytes.

Can Point Defects in Surfaces in Solution be Atomically Resolved by Atomic Force Microscopy?

While the atomic force microscope (AFM) is able to image mineral surfaces in solution with atomic resolution, so far, it has been a matter of debate whether imaging point defects is also possible under these conditions. The difficulties stem from the limited knowledge of what types of defects may be stable in the presence of an AFM tip, as well as from the complicated imaging mechanism involving interactions between hydration layers over the surface and around the tip apex. Here, we present atomistic molecular dynamics and free energy calculations of the AFM imaging of vacancies and ionic substitutions in the calcite (101[over ¯]4) surface in water, using a new silica AFM tip model. Our results indicate that both calcium and carbonate vacancies, as well as a magnesium substitution, could be resolved in an AFM experiment, albeit with different imaging mechanisms.

Understanding 2D atomic resolution imaging of the calcite surface in water by frequency modulation atomic force microscopy

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. 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.

Atomically resolved three-dimensional structures of electrolyte aqueous solutions near a solid surface

Interfacial liquid layers play a central role in a variety of phenomena ranging from friction to molecular recognition. Liquids near a solid surface form an interfacial layer where the molecular structure is different from that of the bulk. Here we report atomic resolution three-dimensional images of electrolyte solutions near a mica surface that demonstrate the existence of three types of interfacial structures. At low concentrations (0.01-1 M), cations are adsorbed onto the mica. The cation layer is topped by a few hydration layers. At higher concentrations, the interfacial layer extends several nanometres into the liquid. It involves the alternation of cation and anion planes. Fluid Density Functional calculations show that water molecules are a critical factor for stabilizing the structure of the interfacial layer. The interfacial layer stabilizes a crystal-like structure compatible with liquid-like ion and solvent mobilities. At saturation, some ions precipitate and small crystals are formed on the mica.

Number density distribution of solvent molecules on a substrate: a transform theory for atomic force microscopy

Atomic force microscopy (AFM) in liquids can measure a force curve between a probe and a buried substrate. The shape of the measured force curve is related to hydration structure on the substrate. However, until now, there has been no practical theory that can transform the force curve into the hydration structure, because treatment of the liquid confined between the probe and the substrate is a difficult problem. Here, we propose a robust and practical transform theory, which can generate the number density distribution of solvent molecules on a substrate from the force curve. As an example, we analyzed a force curve measured by using our high-resolution AFM with a newly fabricated ultrashort cantilever. It is demonstrated that the hydration structure on muscovite mica (001) surface can be reproduced from the force curve by using the transform theory. The transform theory will enhance AFM's ability and support structural analyses of solid/liquid interfaces. By using the transform theory, the effective diameter of a real probe apex is also obtained. This result will be important for designing a model probe of molecular scale simulations.

Molecular Dynamics Simulation of Atomic Force Microscopy at the Water-Muscovite Interface: Hydration Layer Structure and Force Analysis

With the development of atomic force microscopy (AFM), it is now possible to detect the buried liquid-solid interfacial structure in three dimensions at the atomic scale. One of the model surfaces used for AFM is the muscovite surface because it is atomically flat after cleavage along the basal plane. Although it is considered that force profiles obtained by AFM reflect the interfacial structures (e.g., muscovite surface and water structure), the force profiles are not straightforward because of the lack of a quantitative relationship between the force and the interfacial structure. In the present study, molecular dynamics simulations were performed to investigate the relationship between the muscovite-water interfacial structure and the measured AFM force using a capped carbon nanotube (CNT) AFM tip. We provide divided force profiles, where the force contributions from each water layer at the interface are shown. They reveal that the first hydration layer is dominant in the total force from water even after destruction of the layer. Moreover, the lateral structure of the first hydration layer transcribes the muscovite surface structure. It resembles the experimentally resolved surface structure of muscovite in previous AFM studies. The local density profile of water between the tip and the surface provides further insight into the relationship between the water structure and the detected force structure. The detected force structure reflects the basic features of the atomic structure for the local hydration layers. However, details including the peak-peak distance in the force profile (force-distance curve) differ from those in the density profile (density-distance curve) because of disturbance by the tip.

A relationship between three-dimensional surface hydration structures and force distribution measured by atomic force microscopy

Hydration plays important roles in various solid-liquid interfacial phenomena. Very recently, three-dimensional scanning force microscopy (3D-SFM) has been proposed as a tool to visualise solvated surfaces and their hydration structures with lateral and vertical (sub) molecular resolution. However, the relationship between the 3D force map obtained and the equilibrium water density, ρ(r), distribution above the surface remains an open question. Here, we investigate this relationship at an interface of an inorganic mineral, fluorite, and water. The force maps measured in pure water are directly compared to force maps generated using the solvent tip approximation (STA) model and from explicit molecular dynamics simulations. The results show that the simulated STA force map describes the major features of the experimentally obtained force image. The agreement between the STA data and the experiment establishes the correspondence between the water density used as an input to the STA model and the experimental hydration structure and thus provides a tool to bridge the experimental force data and atomistic solvation structures. Further applications of this method should improve the accuracy and reliability of both interpretation of 3D-SFM force maps and atomistic simulations in a wide range of solid-liquid interfacial phenomena.

Atom-resolved analysis of an ionic KBr(001) crystal surface covered with a thin water layer by frequency modulation atomic force microscopy

An ionic KBr(001) crystal surface covered with a thin water layer was observed with a frequency modulation atomic force microscope (FM-AFM) with atomic resolution. By immersing only the tip apex of the AFM cantilever in the thin water layer, the Q-factor of the cantilever in probing the solid-liquid interface can be maintained as high as that of FM-AFM operation in air, leading to improvement of the minimum detection of a differential force determined by the noise. Two types of images with atom-resolved contrast were observed, possibly owing to the different types of ions (K(+) or Br(-)) adsorbed on the tip apex that incorporated into the hydration layers on the tip and on the sample surface. The force-distance characteristics at the solid-water interface were analyzed by taking spatial variation maps of the resonant frequency shift of the AFM cantilever with the high Q-factor. The oscillatory frequency shift-distance curves exhibited atomic site dependence. The roles of hydration and the ions on the tip and on the sample surface in the measurements were discussed.

Ab initio Kinetic Monte Carlo simulations of dissolution at the NaCl-water interface

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. We find that the barrier heights show a systematic reduction from the most stable flat terrace sites, through steps to the smallest barriers for corner and kink sites. Generally, the barriers for removal of Na(+) ions are slightly lower than for Cl(-) ions. Finally, we use our calculated barriers in a Kinetic Monte Carlo as a first order model of the dissolution process.

Three-dimensional hydration layer mapping on the (10.4) surface of calcite using amplitude modulation atomic force microscopy

Calcite, the most stable modification of calcium carbonate, is a major mineral in nature. It is, therefore, highly relevant in a broad range of fields such as biomineralization, sea water desalination and oil production. Knowledge of the surface structure and reactivity of the most stable cleavage plane, calcite (10.4), is pivotal for understanding the role of calcite in these diverse areas. Given the fact that most biological processes and technical applications take place in an aqueous environment, perhaps the most basic - yet decisive - question addresses the interaction of water molecules with the calcite (10.4) surface. In this work, amplitude modulation atomic force microscopy is used for three-dimensional (3D) mapping of the surface structure and the hydration layers above the surface. An easy-to-use scanning protocol is implemented for collecting reliable 3D data. We carefully discuss a comprehensible criterion for identifying the solid-liquid interface within our data. In our data three hydration layers form a characteristic pattern that is commensurate with the underlying calcite surface.

A simple approximation for forces exerted on an AFM tip in liquid

The critical quantity in understanding imaging using an atomic force microscope is the force the sample exerts on the tip. We put forward a simple one-to-one force to water density relationship, explain exactly how it occurs, and in which circumstances it holds. We argue that two wide classes of atomic force microscope (AFM) tip should lead to at least qualitative agreement with our model and represent a significant fraction of AFM tips as currently prepared. This connection between the short-range force and the unperturbed equilibrium water density removes the need to perform simulations for each tip location, conservatively speeding up simulations by around three orders of magnitude compared to current methods that explicitly calculate the force on a tip model at each point in space.

Water and 2-propanol structured on calcite (104) probed by frequency-modulation atomic force microscopy

The structure of liquid water and 2-propanol on the (104) surface of calcite (CaCO3) was probed by frequency-modulation atomic force microscopy. The microscope tip scanned each liquid to record the tip-surface force perturbed by the liquid structure at the interface. In water, the force distribution on planes cross-sectional to the surface presents a 0.5-nm-thick checkerboard-like pattern matching the corrugated topography of the calcite surface. This provides evidence that the local water density was laterally and vertically modulated. With 2-propanol, a laterally uniform, vertically layered structure was found between the first laterally structured layer and the bulk liquid. These results are consistent with the density distributions of water and ethanol proposed in earlier X-ray and simulation studies.

Competitive adsorption on graphite investigated using frequency-modulation atomic force microscopy: interfacial liquid structure controlled by the competition of adsorbed species

The competitive adsorption of long-chain (C18 and C24) carboxylic acids versus n-decanol on graphite was investigated using frequency-modulation atomic force microscopy. A long-range-ordered monolayer of the solute (stearic acid or lignoceric acid) developed in saturated decanol solution, whereas an ordered decanol monolayer was deposited from dilute solutions. The piconewton-order tip-surface force was observed in solutions as a function of the vertical and lateral coordinates, together with the topography of the monolayers. The tip-surface force was periodically modulated, which was interpreted with a solution structure commensurate with the ordered assembly of adsorbed monolayers. These results show that the solution structure at the interface was controlled by the competitively adsorbed species and thus was sensitive to the composition of the bulk solution.

Direct visualization of single ions in the Stern layer of calcite

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). The AFM images provide a direct and atomic-level picture of the different cations adsorbed preferentially at certain locations of the calcite-water interface. Highly ordered water layers at the calcite surface prevent the hydrated ions from directly interacting with calcite due to the energy penalty incurred by the necessary restructuring of the ions' solvation shells. Controlled removal of the adsorbed ions from the interface by the AFM tip provides indications about the stability of the adsorption site. The AFM results show the familiar "row pairing" of the carbonate oxygen atoms, with the adsorbed monovalent cations located adjacent to the most prominent oxygen atoms. The location of adsorbed cations near the surface appears better defined for monovalent ions than for Ca(2+), consistent with the idea that Ca(2+) ions remain further away from the surface of calcite due to their larger hydration shell. The precise distance between the different hydrated ions and the surface of calcite is quantified using MD simulation. The preferential adsorption sites found by MD as well as the ion residence times close to the surface support the AFM findings, with Na(+) ions dwelling substantially longer and closer to the calcite surface than Ca(2+). The results also bring new insights into the problem of the Stern and electrostatic double layer at the surface of calcite, showing that parameters such as the thickness of the Stern layer can be highly ion dependent.