Theoretical Modeling Of Molecular Interactions In Atomic Force Microscope

In the past three decades, Scanning Probe Microscope (SPM), pioneered by Atomic Force Microscope (AFM) recently, have revolutionized the nanotechnology industry, not only because it can provide detailed information about the atomic, chemical, electronic and magnetic structure of the surface with atomic resolution, but more importantly it offers the possibility to directly manipulate atoms and molecules. It is not trivial to interpret the experimental measurements that depend on the atomic structure of the tip apex. In this thesis, AFM measurements operated in frequency modulated non-contact (nc-AFM) mode were performed on the molecular self-assembly and comprehensive knowledge of the tip-sample interaction was gained via Density Functional Theory (DFT) simulations to illustrate the contrast mechanism underping experimental observations. Using experimental and in silico approaches, an in situ tip fingerprinting protocol was proposed and demonstrated, in which the characteristic information of tip candidates could be collected in the measurements of their force responses to a reference surface and compared to the fingerprint database.Dispersion interactions need to be treated carefully in quantitative analysis of molecular interactions using DFT. The orientational dependence of the pair potential of two isolated C60molecules was investigated experimentally and theoretically. The stacking of C6o molecules in the orientational ordered phases of crystal at low temperature was calculated and compared with experimental observations. Basis-set-superposition-error corrected binding energy of two C60molecules is 211-280meV, which agrees well with AFM measurements.Hydrogen bonds underpins the structure and properties of a vast array of systems spanning a wide variety of scientific fields, such as the elegance of base pair interactions in DNA to the symmetry of extended supramolecular assemblies. In this thesis, nc-AFM was used to quantitatively map the tip-sample force field for naphthalene tetracarboxylic diimide (NTCDI) molecules hydrogen-bonded in2D assemblies on Ag:Si(111)-((?)×(?))R30°surface. Using functionalised tip, intermolecular contrast could be observed in AFM images where the hydrogen bonds locate. In DFT simulations, eight tip candidates were considered in calculations and the force spectra over selected surface sites were collected and compared with their experimental counterparts, which shows O down NTCDI tip provides the best intra-and intermolecular contrast. It is found the AFM tip could be negatively charged if it is functionalised by a polar molecule, such as NTCDI or carbon monoxide (CO), and site-specific coulombic repulsion will be enhanced between the negatively charged tip and electron-rich areas on the surface, where the atoms and chemical bonds locate, which could eventually increase image contrast in AFM operated in repulsive region.After the tip functionalisation procedure, the structure of the tip apex becomes more complex. The most obvious obstacle to quantitative measurements in AFM now is that the tip state remains unknown prior to the experiment, during the experiment, even after the experiment. Multiple tip candidates need to be modeled and simulated to analyze the experimental results, which is very computational expensive. In this thesis, a practical two-step experimental strategy is proposed to identify the tips via in situ fingerprinting. Before the identification, ab initio DFT simulations were performed to create a database including the static (force spectra and image contrast) and dynamic responses (dissipation signals) of different tips to a reference surface, i.e. their fingerprints. It is demonstrated in this thesis the possibility to prepare the Si(111)-7×7and Ag:Si(111)-((?)×(?))R30°mixed surface and how to perform tip fingerprinting and submolecularly imaging on the two chemically distinct regions.Diffusion mechanism of small molecules on surface is an area of intense interest. Scanning probe microscopy measurements and DFT calculations were performed to investigate the directional movement of1,3-bi(imidazole-1-ylmethyl)benzene (Walker) on Cu(110) surface. Calculations indicate that unordinary adsorptional geometries lead to the directional motion of walker on the anisotropic Cu surface. Cu atoms on surface covalently bond to the N atoms on imidazolyl groups which function as feet of the walker. Standing with two feet on top of Cu atoms, walker walks on the surface by moving its feet step by step. Minimal energy path analysis reveals that walking along the surface rows involves a low energy barrier of0.15eV and walking across the surface rows involves an energy barrier of0.47eV.