Improvements in microscopy enable the imaging of new phenomena, driving scientific advancement and the technological change it brings. Imaging in ambient conditions in particular can create challenges which limit the resolution. If phenomena can be imaged in an ambient environment the images can be collected more quickly, allowing for faster iteration, and enabling the user to work with samples which cannot enter ultra-high vacuum equipment.

In this thesis, I demonstrate the imaging of transition metal dichalcogenides with atomic resolution conductive atomic force microscopy in ambient conditions and a comparative study alongside optical spectroscopy. Such resolution enables the differentiation of defect categories and the imaging of new types of defects created in samples via exposure to nitrogen plasma. The introduction of defects also induces changes in optical spectroscopy which can be identified in cryogenic measurements. This work builds a strong foundation for future work to establish correlations between the population of defects and features of photoluminescence spectra.

Further work on simulations explores atomic force microscopy techniques for imaging non-planar molecules, demonstrating that constant force approaches could yield high-resolution images of molecules and allow the user to extract quantitative information such as the angle of molecular moieties. Comparisons between experimental and simulated off-resonance atomic force microscope images of a network of Zn tetra-phenyl porphyrin on a Au (111) substrate show promising progress. Such images are created using atomic coordinates from density functional theory simulations and could enable the determination of the adsorption geometry of the molecules in the network in ambient conditions.