As a step toward understanding their functional role, the low frequency vibrational motions (<300 cm ؊1 ) that are coupled to optical excitation of the primary donor bacteriochlorophyll cofactors in the reaction center from Rhodobacter sphaeroides were investigated. The pattern of hydrogen-bonding interaction between these bacteriochlorophylls and the surrounding protein was altered in several ways by mutation of single amino acids. The spectrum of low frequency vibrational modes identified by femtosecond coherence spectroscopy varied strongly between the different reaction center complexes, including between different mutants where the pattern of hydrogen bonds was the same. It is argued that these variations are primarily due to changes in the nature of the individual modes, rather than to changes in the charge distribution in the electronic states involved in the optical excitation. Pronounced effects of point mutations on the low frequency vibrational modes active in a proteincofactor system have not been reported previously. The changes in frequency observed indicate a strong involvement of the protein in these nuclear motions and demonstrate that the protein matrix can increase or decrease the f luctuations of the cofactor along specific directions.Any fundamental description of a biological process must ultimately encompass an account of small and possibly large scale changes in the nuclear geometry of the participating molecules. In particular, a central element in the determination of reaction efficiencies is the structure and accessibility of the transition state, which is the highest point on the free energy barrier that opposes changes in nuclear geometry as the system moves from reactant to product state. For proteins, atoms are most easily displaced along the ''soft'' directionsthe delocalized, low frequency modes-and the study of such motion during a reaction is therefore of particular interest.In recent years, a new aspect of low frequency motion has been revealed by the observation of coherent nuclear motion, persisting on the picosecond (ps) timescale following impulsive optical excitation, and manifested as oscillations in the transient optical properties of the protein cofactors. The discovery of this phenomenon in a variety of protein-cofactor systems, including the bacterial reaction center (RC) (1, 2), bacteriorhodopsin (3), and heme proteins (4), implies that ultrafast biological processes can occur on a timescale that is faster than vibrational relaxation (5). Therefore the possibility of coherent (in addition to thermal) motion along the reaction coordinate must be included in any complete description of a reaction. In addition, the measurement of oscillations by using femtosecond (fs) transient spectroscopy provides a new and convenient method for probing the spectrum of low frequency, nuclear vibrations that are set in motion by a physiological trigger. This study is aimed at assessing the factors that influence the character of such nuclear motions, by exploiting the possibil...