The chemical reaction which creates, destroys, reorganizes chemical bonds to produce new compounds is the most important subject of chemistry. Theoretical/computational studies have come a long way and are now playing the central role in understanding the mechanism and dynamics of chemical reactions and in helping designing more useful chemical reactions and catalysts. I will discuss a few recent examples of our own theoretical/computational studies on chemical reactions of complex molecular systems: (A) self-assembly reactions of small carbon clusters to form fullerenes and carbon nanotubes; (B) homogeneous catalytic reactions and reactions of transition metal and organometallic compounds; and (C) reactions of metalloenzymes and the effects of protein environment.