Engineering topics
Publications and source records attributed to Kim, Tae Wu.
This study explores vibronic wavepacket dynamics in photoinduced electron transfer (PET). The dynamic interplay of PET and coherent wavepacket motions highlights the crucial role of vibrations in influencing efficient PET process.
Bimetallic transition metal complexes have gained increasing attention because of their versatile functions in solar energy conversion and photonics applications arising from inter-metal electronic coupling. In bimetallic platinum (Pt) complexes, electronic communication between the Pt-centered and ligand-centered moieties have been shown to be critical for defining their excited-state dynamic trajectories undergoing either localized ligand centered (LC)/metal-to-ligand-charge-transfer (MLCT) transitions or delocalized metal-metal-to-ligand-charge-transfer (MMLCT) transitions. The branching of the excited-state intersystem crossing (ISC) trajectories are modulated through structural factors that alter the relative energies of the different states. In this study, we investigated the correlation of the structural factors influencing the excited state trajectories. Using femtosecond broadband transient absorption (fs-BBTA) spectroscopy, ultrafast dynamics in the excited state of two select Pt(II) dimers have been mapped out using their coherent vibrational wavepacket signatures in corresponding transient absorption spectra. To examine how the ligand moieties of the Pt(II) dimers influence excited-state dynamics and the coherent vibrational wavepacket behavior, here we carried out comparative studies on two pyrazolate-bridged Pt(II) dimers of the general formula [Pt( t Bu 2 Pz)(N^C)] 2 ( t Bu 2 Pz = 3,5-di-tert-butylpyrazole); N^C = 7,8-benzoquinoline (bzq, 1) or 1-phenylisoquinoline (piq, 2)). We found that photoexcitation into the low energy absorption bands of 1 and 2 respectively induce the formation of 1 MMLCT states from which ultrafast ISC proceeds, resulting in stimulated emission quenching and decoherence of the vibrational wavepacket motions. The results obtained in this study suggest that both energetics and the structural rigidity of the aromatic cyclometalating ligands in 1 and 2 can significantly influence dynamics along the excited state trajectory characterized by dephasing of the coherent oscillations. The collective results provide direct evidence of how ligand structure alters electronic dynamics along excited state trajectories associated with ISC processes, providing insight into using ligand design to steer photochemical processes.
Bacteriophytochromes (BphPs) are photoreceptors that regulate a wide range of biological mechanisms via red light–absorbing (Pr)–to–far-red light–absorbing (Pfr) reversible photoconversion. The structural dynamics underlying Pfr-to-Pr photoconversion in a liquid solution phase are not well understood. We used time-resolved x-ray solution scattering (TRXSS) to capture light-induced structural transitions in the bathy BphP photosensory module of Pseudomonas aeruginosa. Kinetic analysis of the TRXSS data identifies three distinct structural species, which are attributed to lumi-F, meta-F, and Pr, connected by time constants of 95 μs and 21 ms. Structural analysis based on molecular dynamics simulations shows that the light activation of PaBphP accompanies quaternary structural rearrangements from an “II”-framed close form of the Pfr state to an “O”-framed open form of the Pr state in terms of the helical backbones. This study provides mechanistic insights into how modular signaling proteins such as BphPs transmit structural signals over long distances and regulate their downstream biological responses.
In photosynthetic systems employing multiple transition metal centers, the properties of charge-transfer states are tuned by the coupling between metal centers.
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Ultrafast motion of molecules, particularly the coherent motion, has been intensively investigated as a key factor guiding the reaction pathways. Recently, X-ray free-electron lasers (XFELs) have been utilized to elucidate the ultrafast motion of molecules. However, the studies on proteins using XFELs have been typically limited to the crystalline phase, and proteins in solution have rarely been investigated. Here we applied femtosecond time-resolved X-ray solution scattering (fs-TRXSS) and a structure refinement method to visualize the ultrafast motion of a protein. We succeeded in revealing detailed ultrafast structural changes of homodimeric hemoglobin involving the coherent motion. In addition to the motion of the protein itself, the time-dependent change of electron density of the hydration shell was tracked. Besides, the analysis on the fs-TRXSS data of myoglobin allows for observing the effect of the oligomeric state on the ultrafast coherent motion.
A salt bridge, one of the representative structural factors established by non-covalent interactions, plays a crucial role in stabilizing the structure and regulating the protein function, but its role in dynamic processes has been elusive. Here, to scrutinize the structural and functional roles of the salt bridge in the process of performing the protein function, we investigated the effects of salt bridges on the allosteric structural transition of homodimeric hemoglobin (HbI) by applying time-resolved X-ray solution scattering (TRXSS) to the K30D mutant, in which the interfacial salt bridges of the wild type (WT) are abolished. The TRXSS data of K30D are consistent with the kinetic model that requires one monomer intermediate in addition to three structurally distinct dimer intermediates (I 1 , I 2 , and I 3 ) observed in WT and other mutants. The kinetic and structural analyses show that K30D has an accelerated biphasic transition from I 2 to I 3 by more than nine times compared to WT and lacks significant structural changes in the transition from R-like I 2 to T-like I 3 observed in WT, unveiling that the loss of the salt bridges interrupts the R–T allosteric transition of HbI. Besides, the correlation between the bimolecular CO recombination rates in K30D, WT, and other mutants reveals that the bimolecular CO recombination is abnormally decelerated in K30D, indicating that the salt bridges also affect the cooperative ligand binding in HbI. These comparisons of the structural dynamics and kinetics of K30D and WT show that the interfacial salt bridges not only assist the physical connection of two subunits but also play a critical role in the global structural signal transduction of one subunit to the other subunit via a series of well-organized structural transitions.
One of the most challenging tasks in biological science is to understand how a protein folds. In theoretical studies, the hypothesis adopting a funnel-like free-energy landscape has been recognized as a prominent scheme for explaining protein folding in views of both internal energy and conformational heterogeneity of a protein. Despite numerous experimental efforts, however, comprehensively studying protein folding with respect to its global conformational changes in conjunction with the heterogeneity has been elusive. Here we investigate the redox-coupled folding dynamics of equine heart cytochrome c (cyt-c) induced by external electron injection by using time-resolved X-ray solution scattering. A systematic kinetic analysis unveils a kinetic model for its folding with a stretched exponential behavior during the transition toward the folded state. With the aid of the ensemble optimization method combined with molecular dynamics simulations, we found that during the folding the heterogeneously populated ensemble of the unfolded state is converted to a narrowly populated ensemble of folded conformations. These observations obtained from the kinetic and the structural analyses of X-ray scattering data reveal that the folding dynamics of cyt-c accompanies many parallel pathways associated with the heterogeneously populated ensemble of unfolded conformations, resulting in the stretched exponential kinetics at room temperature. This finding provides direct evidence with a view to microscopic protein conformations that the cyt-c folding initiates from a highly heterogeneous unfolded state, passes through still diverse intermediate structures, and reaches structural homogeneity by arriving at the folded state.
Abstract not provided