The work in this thesis is basically divided into two related but separate investigations.

The first part treats simple chemical reactions of adsorbate molecules on metallic surfaces, induced by means of a scanning tunneling probe (STM). The investigation serves as a parameter free extension to existing theories. The theoretical framework is based on a combination of density functional theory (DFT) and non-equilibrium Green's functions (NEGF). Tunneling electrons that pass the adsorbate molecule are assumed to heat up the molecule, and excite vibrations that directly correspond to the reaction coordinate. The theory is demonstrated for an OD molecule adsorbed on a bridge site on a Cu(110) surface, and critically compared to the corresponding experimental results. Both reaction rates and pathways are deduced, opening up the understanding of energy transfer between different configurational geometries, and suggests a deeper insight, and ultimately a higher control of the behaviour of adsorbate molecules on surfaces.

The second part describes a method to calculate STM images in the low bias regime in order to overcome the limitations of localized orbital DFT in the weak coupling limit, i.e., for large vacuum gaps between a tip and the adsorbate molecule. The theory is based on Bardeen's approach to tunneling, where the orbitals computed by DFT are used together with the single-particle Green's function formalism, to accurately describe the orbitals far away from the surface/tip. In particular, the theory successfully reproduces the experimentally well-observed characteristic dip in the tunneling current for a carbon monoxide (CO) molecule adsorbed on a Cu(111) surface. Constant height/current STM images provide direct comparisons to experiments, and from the developed method further insights into elastic tunneling are gained.