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In this thesis a range of phenomena related to molecular adsorption on silicon surfaces is investigated. The majority of the studies are performed in response to experimental results, where, using newly developed methods within the framework of density functional theory, we aim to elucidate some of the underlying physics as well as test the performance of the chosen methodology. The studies cover a range of subjects such as molecularly mediated pinning of surface geometry, single molecular adsorptions, molecule migration via exited states and finally an analysis of coverage dependent adsorption phenomena, where interactions between molecules are mediated by the surface or enacted via dipole interactions. The main molecules of our simulations were water, ethylene, acetylene, and benzene, as well as halogenated hydrocarbons. We studied processes at two different surfaces, the Si(111)-7 x 7 surface, and the Si(100)-c(4 x 2) surface. Finally we simulated and characterized one type of grain boundary observed experimentally for a set of photovoltaic absorbers (CuInSe_{2}) and kesterite and stannite(Cu_{2}ZnSnSe_{4} or Cu_{2}ZnSnS_{4}) in order to resolve the open question of how these grain boundaries influence efficiencies of the photovoltaic device.