Multireference as well as density functional theories in combination with the surface integrated molecular orbital molecular mechanics were adopted to study the surface reactions of cyanogens on Si(100)-2x1 surface. Three different products were identified as minima in the initial surface reaction. Among these, the [2+2] product is both kinetically easily accessible and thermodynamically the most stable. Therefore, it can be considered as the experimentally found strongly bound surface species. Unlike other conjugated systems, the [4+2] product is less stable than the [2+2] product. Subsequent surface isomerization studies revealed that kinetically favorable channels exist between the initially formed low-temperature species and the high-temperature species, indicating that surface morphology changes gradually as a function of surface temperature. Theses two channels eventually lead to the same final surface products, which is consistent with experiment. Current study shows that the subsequent surface isomerizations are the key reactions to better understand the complex surface structures and their properties. (C) 2004 American Institute of Physics.