Structural and electronic dynamics studies of photoactive macromolecules using time-resolved X-ray scattering and optical spectroscopy

Abstract

Photoactive macromolecules play many essential roles in regulating a biological or chemical function in living organism or light harvesting system. The photoactive bio-macromolecules such as protein or nucleic acid have its own photoreaction accompanying the change in the three-dimensional structures (or conformations). The structural transitions of bio-macromolecule mediate the expression of characteristic biological function. The organic or inorganic macromolecules acting as artificial light harvesting module has the photodynamics of excited charge carrier generated from the light illumination. This excited carrier dynamics in an artificial light harvesting module is highly related with the efficiency of solar-energy conversion. Accordingly, it is of importance to investigate both of the structural dynamics and the excited carrier dynamics of photoactive macromolecule. Despite the importance, the comprehensive study for the structural and electronic dynamics of macromolecular system is elusive due to the lack of adequate experimental technique with the high time-resolution. The research works in this dissertation mainly focus on the direct observation of structural and electronic dynamics of macromolecular system covering from photoactive protein to artificial light harvesting system. To do so, the various time-resolved (or pump-probe) techniques are employed. Time-resolved X-ray solution scattering with optical pump and X-ray probe has a superb structural sensitivity com-pared with the time-resolved optical spectroscopy. In contrast, the combination of optical pump and optical probe pulse in time-resolved optical spectroscopy sensitively detects the change of the electronic state induced by the pump pulse. Thus, the combination of time-resolved X-ray solution scattering (TRXSS) and time-resolved optical spectroscopy enable us to directly track the electronic and structural change of intermediate in the photoreaction of macromolecular system. TRXSS experiment for the signaling of wild-type photoactive yellow protein (wt-PYP) is implemented. From the systematic kinetic analysis of time-resolved X-ray scattering data, the parallel kinetics including the four intermediates is determined. Using the shape reconstruction of intermediate, the information for the molecular shape of intermediate can be extracted from the species-associated scattering curve. From the structural analysis, it is revealed that the signaling of wt-PYP accompanies a protrusion of N-terminal which is maximized in the signaling state. This conformational change of wt-PYP in solution cannot be detected in the crystalline phase due to the crystal contact. The time-resolved X-ray solution scattering experiment of wt-PYP demonstrates the possibility that TRXSS is an adequate method to track the protein conformational change in real time. The combination of TRXSS sensitive to the protein conformation and time-resolved optical spectroscopy sensitive to the environment of photosensory domain (or chromophore) is used to investigate the relationship between the local structural transition around chromophore and the change in the global protein con-formation. From the combined probe approach, it is unraveled that in the site-directed mutant PYP (E46Q-PYP) the local structure of the chromophore probed by time-resolved optical spectroscopy temporally pre-cedes the change in the global conformation leading to the signaling state probed by TRXSS. This combined probe approach gives us the information for the local structural change around the chromophore as well as the global conformational change. The target bio-macromolecule of TRXSS experiment is expanded to phytochrome which is an oligomer protein acting as a red-light photoreceptor in plants, fungi, and bacteria. The analysis of time-resolved scattering signal based on the non-equilibrium molecular dynamics simulation sheds light on the new structural insight into the signaling transduction mechanism of bacteriophytochrome. The expression of signaling state in the photocycle of bacteriophytochrome involves the formation of large void in the middle of protein through the opening of two helical spines. This result suggests that the protein conformational change of bathy bacteriophytochrome is quite different with that of canonical bacteriophytochrome. To investigate the excited carrier dynamics on the inorganic semiconductor, the femtosecond transient absorption spectroscopy experiment of size-graded PbS colloidal quantum dots (CQDs) is performed. From the comparative study between the size-graded CQDs and the single-sized CQDs, it is demonstrated that the excited carrier transfer between the layers containing different sizes of CQDs is accelerated in size-graded case relative to in single-sized case. Considering the energy diagram on size-graded CQDs, the feature of the accelerated excited carrier transfer is originated from the quantum funnel effect. The effect of nitrogen atom introduced in the conjugated polymer is investigated by using the various experimental techniques probing from the morphology to the excited state character of conjugated polymer. The transmission electron microscopy measurement shows that the presence of nitrogen heteroatom does not alter the morphology of conjugated polymer. However, the presence of nitrogen heteroatom in conjugated polymer results in the detrimental effect in the power conversion efficiency, which is connected with the fast charge recombination dynamics in the transient absorption signal. From the time-dependent density functional theory of polymer moiety, it is unraveled that the nitrogen heteroatom in conjugated polymer decreases the polarity of conjugated polymer represented by the excited state dipole, resulting in the decrease of the extent of charge separation.