The monograph, based mainly on the results of the author, is devoted to a consistent presentation of the approach to describing the chemical transformations of complex molecules (structural isomerization, bimolecular processes of addition and decomposition) as a consequence of temperature and photoexposure. The formalism of the approach is built as an extension of the theory of electron-vibrational spectra of polyatomic molecules. Appropriate energy matrices suitable for characterizing states of complex systems and new processes are introduced. Analysis of the consequences of the general theory allows us to formulate simple rules for the course of chemical transformations and path finding. Examples of such studies are given.