First, the parameter-dependent zeroth-order basis (PDZOB) method was employed in the study of the quantum mechanical dynamics of a HCN/HNC isomerization model reaction for a few hundred femtoseconds before the time of the unimolecular reaction. From this study, it was learned that the dominant mode-mode specific energy flow incorporated with large and sudden energy transfer is responsible for the isomerization. The classical dynamics study of the same isomerization also reveals the mode-mode specific impulsive energy transfer. Second, the HEG-Wigner distribution (HEGWD) method was applied to study phase space in the quantum dynamics of a two-mode hindered rotor isomerization. We discovered that regularity in the phase space lasts for about 200 fs after the initiation of this reaction. Strong correspondence between the semi-classical result with ℏ = 0.5 and that in the classical result has been observed; however, there was no clear correspondence between the full-quantum result with ℏ = 1.0 and the classical result.