Since the invention of the transmission electron microscope (TEM) in 1931 by Max Knoll and Ernst Ruska, modern TEMs underwent remarkable developments in its overall stability and electron optics. In particular, correction of higher-order lens aberrations has facilitated structural characterization of single molecules at atomic resolution. This improvement in resolution has greatly assisted the design and development of new nano-objects in the field of materials and biological sciences. However, taking full advantage of these developments requires high chemical purity in the sample preparation technique and an electron transparent sample support that not only ensures the reliability in structural characterization, but also boosts the signal-to-noise ratio of TEM images. Moreover, the electron beam in TEMs, in addition to image formation, can be used for structural transformation due to the strong interaction of electrons with the investigated material.

In this thesis, the structure of mass-selected molecular species, deposited on graphene via electro-spray ion beam deposition (ES-IBD), is investigated by aberration-corrected high-resolution transmission electron microscopy (AC-HRTEM) at acceleration voltages between 60 and 80 kV. Due to its impressive electronic and mechanical properties, single- layer graphene (SLG) is used as TEM substrate throughout this work. The transfer methodology of the SLG, obtained by mechanical exfoliation or chemical vapor deposition (CVD), to the TEM grids is presented, followed by thorough structural characterization to analyze the morphology and crystallinity of the transferred SLG using HRTEM. First, beam-sensitive organic molecules such as cytochrome-class hemeprotein (cytochrome-c), chaperonin complex protein molecule (GroEL), copper-pthalocyanine (CuPc) and com- plex molecular magnetic systems in the form of single molecule magnets (SMMs) were investigated. The results showed that despite the presence of the highly conductive substrate and the use of low electron acceleration voltages, small organic molecules did not survive. However, large globular proteins showed some level of electron resistance before suffering radiation damage.

Next, the molecular structure of single phosphotungstic acid (PTA) anion molecules deposited by either ES-IBD or the drop-cast method was analyzed and compared. The results showed homogeneous morphology of the samples prepared by ES-IBD. Further- more, by varying coverage and landing energy, it was possible to modify the required morphology. This allowed better control of deposition as compared to the drop cast ap- proach. A main advantage of ES-IBD is the chemical purity during deposition. This is not guaranteed in the drop-cast technique which is performed under ambient conditions. The main part of this thesis deals with the electron-beam-induced transformation of alkali-iodide molecules (CsI, RbI, KI and NaI). The deposited alkali iodide nanoparticles were intentionally exposed to the electron beam to disintegrate them into single ions. It is found that during electron exposure these ions form regular clusters consisting of 4 to 7 atoms, or 2D-crystals. Notably, in the case of CsI, 2D-crystals form only on BLG, whereas on SLG only atomic clusters were formed. HRTEM in combination with electron energy-loss spectroscopy (EELS) is employed to identify the atomic species of the 2D crystals on the atomic scale. In the case of NaI, 2D-crystals form on SLG. Their crystal structure corresponds to the CsCl-type, which has not been reported before.

The etching behavior of graphene in the presence of alkali-iodide species is observed in HRTEM experiments for all the deposited species (CsI, RbI, KI, and NaI). By mea- suring the increase in the perimeter of etched holes in SLG, the rate of etching has been calculated. We found that etching was faster in the presence of both alkali and halide ions, as compared to the presence of only one ionic species. First-principles DFT simulation studies were performed to understand the interaction of alkali-iodide dimers on SLG. These calculations yielded quantitative estimates on the charge transfer between the dimer species and the underlying SLG. It was found that adsorption of alkali-iodide on SLG reduces the bonding electron density between the carbon atoms, thus reducing the C-C binding energy. This effect makes the SLG susceptible to damage when exposed to 80-keV electrons, which establishes the catalytic behavior of alkali-iodide species as etchants of SLG.