Basic knowledge of mankind so far relates to the description of electrons and atoms in the material in a state of equilibrium, where the behavior changes slowly over time. The electron diffraction with a high temporal and space resolution has opened the possibility of direct observation of the processes occurring in the transient state of the substance (molecular movie). Here it is necessary to provide a temporary resolution of the order of 100 fs, which corresponds to the transition of the system through the energy barrier of the potential surface, which describes the chemical reaction - the process of the breaking and the formation of new bonds between the interacting agents. Thus, the possibility of the investigation of the coherent nuclear dynamics of molecular systems and the condensed matter can be opened. In the past two decades, it has been possible to observe the nuclear motion in the temporal interval corresponding to the period of the nuclear oscillation. The observed coherent changes in the nuclear system at such temporal intervals determine the fundamental shift from the standard kinetics of chemical reactions to the dynamics of the phase trajectory of a single molecule, the molecular quantum state tomography.