The main body of this thesis describes how to calculate scanning tunneling microscopy (STM) images from first-principles methods. The theory is based on localized orbital density functional theory (DFT), whose limitations for large-vacuum STM models are resolved by propagating localized-basis wave functions close to the surface into the vacuum region in real space. A finite difference approximation is used to define the vacuum Hamiltonian, from which accurate vacuum wave functions are calculated using equations based on standard single-particle Green’s function techniques, and ultimately used to compute the conductance. By averaging over the lateral reciprocal space, the theory is compared to a series of high-quality experiments in the low- bias limit, concerning copper surfaces with adsorbed carbon monoxide (CO) species and adsorbate atoms, scanned by pure and CO-functionalized copper tips. The theory compares well to the experiments, and allows for further insights into the elastic tunneling regime.

A second significant project in this thesis concerns first-principles calculations of a simple chemical reaction of a hydroxyl (oxygen-deuterium) monomer adsorbed on a copper surface. The reaction mechanism is provided by tunneling electrons that, via a finite electron-vibration coupling, trigger the deuterium atom to flip between two nearly identical configurational states along a frustrated rotational motion. The theory suggests that the reaction primarily occurs via nuclear tunneling for the deuterium atom through the estimated reaction barrier, and that over-barrier ladder climbing processes are unlikely.