Mapping Structural Dynamics of Proteins with Femtosecond Stimulated Raman Spectroscopy

The structure-function relationships of biomolecules have captured the interest and imagination of the scientific community and general public since the field of structural biology emerged to enable the molecular understanding of life processes. Proteins that play numerous functional roles in cellular processes have remained in the forefront of research, inspiring new characterization techniques. In this review, we present key theoretical concepts and recent experimental strategies using femtosecond stimulated Raman spectroscopy (FSRS) to map the structural dynamics of proteins, highlighting the flexible chromophores on ultrafast timescales. In particular, wavelength-tunable FSRS exploits dynamic resonance conditions to track transient-species-dependent vibrational motions, enabling rational design to alter functions. Various ways of capturing excited-state chromophore structural snapshots in the time and/or frequency domains are discussed. Continuous development of experimental methodologies, synergistic correlation with theoretical modeling, and the expansion to other nonequilibrium, photoswitchable, and controllable protein systems will greatly advance the chemical, physical, and biological sciences.

Femtosecond infrared pump-stimulated Raman probe spectroscopy: the first application of the method to studies of vibrational relaxation pathways in the liquid HDO/D2O system

We have proposed and constructed a setup for a novel method of ultrafast vibrational spectroscopy: femtosecond infrared pump-stimulated Raman probe spectroscopy. This is the first time-resolved spectroscopy providing simultaneously a sub-100 fs time resolution, a spectral resolution better than 10 cm^-1 and a spectral window covering an extremely broad range of molecular vibrations (at least: 200-4000 cm^-1) with a "single laser shot". The new method was applied to study vibrational relaxation pathways in the liquid HDO/D₂O system. We determined the lifetimes of OH stretching vibrations to be in the range 310-500 fs depending on the isotopic dilution, which is in good agreement with the results from pump-probe femtosecond infrared spectroscopy. Moreover, we observed a strong coupling of OH stretch to OD stretch vibrations and possibly also to the librational modes of water.

Exploring laser-driven quantum phenomena from a time-frequency analysis perspective: a comprehensive study

Time-frequency (TF) analysis is a powerful tool for exploring ultrafast dynamics in atoms and molecules. While some TF methods have demonstrated their usefulness and potential in several quantum systems, a systematic comparison among them is still lacking. To this end, we compare a series of classical and contemporary TF methods by taking hydrogen atom in a strong laser field as a benchmark. In addition, several TF methods such as Cohen class distribution other than the Wigner-Ville distribution, reassignment methods, and the empirical mode decomposition method are first introduced to exploration of ultrafast dynamics. Among these TF methods, the synchrosqueezing transform successfully illustrates the physical mechanisms in the multiphoton ionization regime and in the tunneling ionization regime. Furthermore, an empirical procedure to analyze an unknown complicated quantum system is provided, suggesting the versatility of TF analysis as a new viable venue for exploring quantum dynamics.