The scope of this work can be described as a multi-scale study of the properties of organic molecules and films on bulk insulating surfaces. This study incorporates a multi-scale
model that provides unambiguous interpretation of experimental data. This allowed me to validate my results describing the properties of single molecules on insulating surfaces, characterize adsorption, and discuss the mechanisms behind experimentally observed phe-nomena. I then focused on expanding the time-scale and size-scale of my simulations to probe dynamic effects and predict the structures of monolayers on the surface.
In this thesis I start by presenting general theoretical methods that are relevant to more than one results chapter in Chapter 2. I cover density functional theory (DFT), classical force fields, and the hybrid quantum mechanics/molecular mechanics (QM/MM) techniques which can be used to describe molecule-surface interactions. Special attention is paid to common difficulties and nonstandard methods that I used to greatly reduce the computational cost of treating my systems. I then briefly discuss the molecular dynamics (MD) methods that I used to expand the time-scale of my studies.
The results chapters are then presented in the following order. Each chapter starts with a general introduction which includes a review of the latest methods, prior work, a description of the challenge that I set out to address, and outlines novelty of my work. The logical first step to these studies was to examine what happens when an atom or molecule first lands on the surface and the effects this may have on the distribution of single atoms (or molecules) and their ability to reach surface features, such as step edges. With this in mind, I studied the mechanisms of transient mobility using a simple model system. Pd atoms were deposited on the MgO(001) surface using classical pair potentials and molecu-lar dynamics at experimentally feasible conditions. The simple atomic system allowed me to perform a large number of simulations of sufficiently long duration to characterize the mechanisms that are responsible for transient mobility. The data was compared and ana-lyzed in the context of prior experiments and theory in the fields of scattering, tribology, growth kinetics, and diffusion. This work is discussed in Chapter 3 of this thesis.
I then moved on to examine the properties of adsorbed single molecules on oxide sur-faces in Chapter 4. This work provided an opportunity to study quantum mechanical methods and other techniques needed to investigate organic molecules and metal-organic
complexes on oxide surfaces. I was able to compare my results to experimental images as part of a collaboration with A. Schwarz, J. Grenz, and R. Wiesendanger at the Univer-sity of Hamburg. Co-Salen (a Co containing metal-organic complex) was deposited onto NiO(001) and studied using NCAFM in combination with DFT in order to examine the differences in adsorption and growth on various bulk insulator surfaces. By combining the-ory and experiment in this system, I was able to determine the adsorption site of Co-Salen on NiO(001) and provide an explanation for the differences observed in comparison to a previous study of Co-Salen on NaCl(001) [3]. My results highlight the qualitative differ-ences that arise due to slight changes in commensurability on the two surfaces despite the fact that both are bulk insulators with the same simple cubic crystal structure.
While these results were in good agreement with my initial interpretation of the ex-perimental data, the imaging mechanism and the properties of the NCAFM tip used in these studies still needed to be explored. To accomplish this I studied the properties of the metal coated NCAFM tip to develop a point dipole model for the tip. Then I directly simulated NCAFM experiments by combining this point dipole model with a virtual AFM (VAFM) code. This multi-scale method was tested by studying adsorbed CO molecules on NiO(001) and shown to provide quantitative agreement with experimental data. The point dipole model and these results are discussed in Chapter 5.
I then moved on to study the structure of self-assembled monolayers of 1,4-bis(cyanophenyl)-2,5-bis(decyloxy)benzene (CDB) molecules on KCl(001) in Chapter 6. This work was part of a collaboration with NCAFM experimentalists C. Loppacher and L. Nony at Aix-Marseille University. Using DFT methods, I characterized the competing molecule-molecule and molecule-molecule-surface interactions within the system. This data then allowed me to propose atomistic models for experimentally observed monolayer patterns. I compared the energies of these structures to identify the most stable configuration. This configura-tion was then used to generate VAFM images using the point dipole model which could be directly compared to experimental images. However, despite good agreement between experimental and theoretical images, initial ab initio molecular dynamics simulations
pre-dicted that the molecules are quite dynamic on the surface. A static picture is somewhat misleading, especially since the experimental data was taken at room temperature. Unfor-tunately, I was unable to investigate these properties or the diffusion, trapping, and growth of these molecules using DFT due to the prohibitively expensive computational cost.
In order to study dynamic effects, the scale of the system had to be substantially increased in several ways. The number of molecules had to be increased in order to avoid imposing heavy constraints on the system. The time-scale had to be greatly increased to study slower processes, such as growth and nucleation. These kinds of simulations are typically performed using classical molecular dynamics, however, there were no readily available molecule-surface force fields for my system. My solution was to fit a set of molecule-surface interactions to ab initio data by using genetic algorithm (GA) methods.
I was then able to study diffusion, adhesion to step edges, and dewetting to gain insight into some of the dynamic properties of the system. The scheme I employed to generate molecule-surface forcefields is presented in Chapter 7 along with these results.
Finally, the results of these studies are summarized and discussed in Chapter 8 and suggestions are made for future work.