Using density functional theory calculations, we have studied structural models, reaction mechanisms and electromagnetic properties of various nanostructures on semiconductor surfaces. We have investigated structural model of H2 dissociative adsorption on Si(001) as a prototype of molecular reaction on semiconductor surface. The dissociative adsorption of an H2 molecule on the Si(001) surface has been experimentally identified in terms of dissociation on one side of two adjacent Si dimers. In contrast to the prevailing nonmagnetic configuration of charge ordering, we propose a new ground state where the two single DBs created by H2 dissociation are antiferromagnetically coupled with each other. We also have studied a self-assembly of one dimensional molecular lines on Si(001). We have proposed various self-assembly method for fabrication of the molecular lines such as heterogeneous molecular lines and stable molecular lines by using H-free dimer as a reaction site. We also found exotic electronic properties and growth mechanisms of the 1D molecular lines.