The development of computers has facilitated to calculate the molecular structures and chemical reactions on the basis of the theories of physics. As a result, it became possible to easily examine the structure and property of the molecule, energy profile of the reaction, and so on, which is difficult by the experiment. Therefore, we can understand the chemical phenomena at the molecular level. Through the theoretical calculation, we can experience that the natural phenomena is originated to the molecular structure and property. In our laboratory, we are working on the analysis, prediction and design by the theoretical calculation, for the molecules with a simple structure to a complex one. We also develop the methods of analysis and propose and apply the new molecular theories.