Simulation of Subnanometer Contrast in Dynamic Atomic Force Microscopy of Hydrophilic Alkanethiol Self-Assembled Monolayers in Water

Abstract

Atomic resolution imaging of surfaces in liquid environments using atomic force microscopy (AFM) is challenging in terms of both reproducibility and measurement interpretation. To understand the origins of these challenges, we used molecular dynamics simulations of AFM on hydrophilic self-assembled monolayers (SAMs) in water. The force on the model AFM tip was calculated as a function of lateral and vertical position relative to the SAM surface. The contributions of the water and SAMs to the overall force were analyzed, and the former was correlated to the water density distribution. Then, dynamic AFM was modeled by oscillating the tip at a driving amplitude. It was found that the contrast between amplitudes at different lateral positions on the surface was dependent on the vertical position of the tip. Lastly, amplitude maps were produced for two vertical positions at constant height, and the ability to capture atomic resolution was related to the force on the tip. These results offer an explanation for the observed instability in atomic scale imaging using AFM and more generally provide insight into the contrast mechanisms of surface images obtained in liquid environments.

Subnanometer Interfacial Forces in Three-Dimensional Atomic Force Microscopy: Water and Octane near a Mica Surface

“…The experimental results were accompanied by a variety of theoretical studies and molecular dynamics simulations. Computer modeling was focused on providing an understanding of the origin of the atomic-scale contrast observed in the images − and on the determination of the role of the hydration structure on the tip on the imaging . Several models and theories were proposed to relate the liquid density distributions to the interfacial forces. − In this context, little theoretical effort was devoted to understanding the role and interplay between the properties of the bulk liquid and the properties of the solid–liquid interaction.…”

Simulations of Friction Anisotropy on Self-Assembled Monolayers in Water

“…58 The details of model construction were described in our previous studies. 35,59,60 Briefly, the water molecules were modeled using the extended simple point charge potential (SPC/E). 61 The sulfur−gold interactions were modeled using the Morse potential 62,63 while the Lorentz−Berthelot mixing rules 64 and the Lennard-Jones potential 65 were used for all other long-range interactions.…”

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

“…The primary challenge with understanding contrast mechanisms lies in the difficulty of understanding the interactions between the tip, water, and sample . When samples are immersed in water, tip–sample, tip–water, and water–sample forces affect the dynamic response of the cantilever.…”

“…One approach to investigating contrast mechanisms in AFM is molecular dynamics (MD) simulation. ,, MD simulations capture atomic scale interactions, but are computationally inexpensive, which allows modeling large and complex systems, as well as the dynamic aspects of the AFM measurement. For example, experimental contrast patterns of calcite in water were reproduced using MD simulations with variable tip–sample distance and driving amplitude .…”

“…One study used MD simulations to investigate how tip interactions with SAMs at different lateral positions affected image contrast in vacuum . Our previous study simulated AFM on a hydroxyl terminated SAM and showed that contrast on SAMs in water strongly depended on interactions with both the sample and the water . Here, we used MD simulations of an AFM tip apex and SAMs immersed in water to investigate the effect of surface functional groups and chain length on subnanometer scale image contrast.…”