The low-frequency vibrational coherence from Zn(II)-substituted cytochrome c (ZnCytc) was characterized at room temperature in the native and acid/high-salt molten-globule states using femtosecond pump-probe, dynamic-absorption spectroscopy and impulsive excitation of the Soret absorption band. The pump-probe signals observed from the native state contain two types of modulation components in the vibrational coherence. The first type is a set of slowly damped (damping time γ > 1.5 ps) components with frequencies of 10, 30, 70, and 120 cm(-1) that are assigned to out-of-plane vibrations of the porphyrin macrocycle following similar assignments in other porphyrin systems. A similar set of components is observed in the pump-probe signal from the molten-globule state, but the signal is much less strongly modulated. The second type is a strong, very rapidly damped (γ < 150 fs) 79 cm(-1) modulation component that is assigned to van der Waals interactions between the porphyrin and nonpolar groups in its first solvation shell from the surrounding protein structure; the line shape and intensity of this component are comparable to those observed previously for bacteriochlorophyll a and Zn(II)meso-tetrakis(N-methylpyridyl)porphyrin in solution. This component is almost completely absent from the signal from the molten-globule state. The results suggest that the van der Waals modes obtain intensity enhancement in the vibrational coherence because the attacking groups are displaced by the change of extent and/or change in shape of the π-electron density that accompanies the π → π* optical transition of the Zn(II) porphyrin. In the molten-globule state of ZnCytc, owing to the expanded hydrophobic core and to the loss of order for the groups that attack the π-electron density of the Zn(II) porphyrin, the van der Waals modes are rendered effectively inactive. These results support an assignment of the broad low-frequency background in the spectrum of the vibrational coherence in purple bacterial photosynthetic reaction centers to van der Waals interactions between the primary electron donor, P, and the nonpolar protein-derived groups in its first solvation shell.