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Scanning tunneling microscopy (STM) is a powerful and widely used instrument to probe atomic features on conductive surfaces. The STM can operate in many environments; however, at extreme conditions such as at liquid He temperatures and in ultra-high vacuum (UHV)-low-temperature UHV STM offers a clean reaction environment to study the chemistry to structures at the single-molecule level. In such operating conditions, the reaction environment can be controlled and fine-tuned to the experimental necessities. At the vacuum-solid interface, the operator can introduce a specific amount and type of chemical species onto the surface to probe single-molecule chemistry. A detailed analysis on the chemistry to structures at the single-molecule level for dimethyl disulfide (DMDS) and Ni(salophen) deposited on the Au (111) surface has been explored by low-temperature UHV STM. Dimethyl disulfide dissociation via UV and STM tip pulses has been explored with dissimilar separation distances. Supramolecular assemblies of DMDS as a function of concentration and temperature at the Au (111) surface reveal different surface morphology suggesting process and concentration dependent nucleation. The nature of DMDS adsorption onto the Au (111) surface is detailed to have a kinetic nature rather than thermodynamic. The chemistry to structures of Ni(Salophen) have also been explored in UHV. We present the spectroscopic nature of the supramolecular assembly of Ni(salophen) molecules on the surface by probing the HOMO and LUMO levels at the vacuum-solid interface. These spectroscopic measurements are the next stage of surface characterization with aims to provide insight on the physical and electronic properties of the adsorbed chemical species with direct single-molecule precision measurements. The chemical experiments above have a profound impact on relating the chemistry to the structure of the adsorbed molecules on the Au (111) surface. Scanning tunneling microscopy is a powerful tool which enables rich characterization of surface properties at the single-molecule level.
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