The paper focuses on the study of transformation of silicon crystal into silicon carbide crystal via substitution reaction with carbon monoxide gas. As an example, the Si(1 0 0) surface is considered. The cross section of the potential energy surface of the first stage of transformation along the reaction pathway is calculated by the method of nudged elastic bands. It is found that in addition to intermediate states associated with adsorption of CO and SiO molecules on the surface, there is also an intermediate state in which all the atoms are strongly bonded to each other. This intermediate state significantly reduces the activation barrier of transformation down to 2.6 eV. The single imaginary frequencies corresponding to the two transition states of this transformation are calculated, one of which is reactant-like, whereas the other is product-like. By methods of quantum chemistry of solids, the second stage of this transformation is described, namely, the transformation of precarbide silicon into silicon carbide. Energy reduction per one cell is calculated for this ‘collapse’ process, and bond breaking energy is also found. Hence, it is concluded that the smallest size of the collapsing islet is 30 nm. It is shown that the chemical bonds of the initial silicon crystal are coordinately replaced by the bonds between Si and C in silicon carbide, which leads to a high quality of epitaxy and a low concentration of misfit dislocations.