For full understanding of the molecular mechanisms of enzymatic reactions, it is crucial to obtain the detailed structural information of the active sites of proteins. Reaction-induced Fourier transform infrared (FTIR) difference spectroscopy, which detects minute changes in the infrared absorption upon some reaction, is a powerful method to investigate the structures and reactions in the active sites of proteins at the atomic and molecular levels. In particular, light-induced FTIR difference spectroscopy that uses light as a trigger to initiate reactions has been extensively used in the studies of molecular mechanisms of photosensitive proteins. In this review article, the methods of measurement and analysis of light-induced FTIR difference spectra are described and applications to the studies of photosensitive proteins are introduced.
Nonlinear vibrational spectroscopy by use of mid-infrared femtosecond pulses enables the observation of ultrafast vibrational/structural dynamics of molecular systems. This article presents the recent experimental studies on vibrational energy relaxations and energy transfer in liquid water. In pure liquid water, vibrational energy relaxation of OH-stretching and OH-bending excitation occurs at about 200fs and 170fs, respectively. When vibrational energy from individually excited water molecules is transferred to intermolecular modes, a sub-100fs nuclear rearrangement occurs, leaving the local hydrogen bonds weakened but unbroken. Subsequent energy delocalization over many molecules proceeds with the breaking of hydrogen bonds on an 1-ps time scales. The observed vibrational/structral response should be relevant for chemical reactions and structural changes in aqueous environments.
Recently, studies of phonons by inelastic x-ray scattering (IXS) technique with a high energy resolution of meV order have considerably developed by using an excellent technique for utilizing third-generation synchrotron radiation facilities and recent progress of semiconductor technique. In this article, the history of studies of phonons using x-rays, the principle of IXS and the advantage (disadvantage) of IXS are briefly reviewed by comparing to inelastic neutron scattering, and an excellent IXS spectrometer installed at the beamline BL35XU of the SPring-8 is introduced. Finally, examples of recent studies performed at BL35XU/SPring-8 are introduced in mainly disordered systems.