Research
Overview
The most intuitive approach to unveiling reaction mechanisms is real-time tracking of the three-dimensional structure of molecules involved in a chemical reaction. We utilize time-resolved x-ray scattering to visualize the structural changes of molecules, capturing a dynamic “molecular movie”, which allows us to identify precise reaction pathways and mechanisms. This method is not limited to small molecules but can also be applied to macromolecules such as proteins, enabling real-time tracking of structural changes in proteins during biologically-relevant reactions. Our ultimate goal is to provide fundamental information on the mechanism of various chemical reactions, which can be valuable for optimizing catalytic efficiency and controlling reaction products. Furthermore, by elucidating the correlation between protein structure and function, we can also gain insights into various biological phenomena and diseases caused by abnormal protein interactions.
Research Topics
How to Capture Atomic Motion
When chemical and biological reactions occur, observing the movement of atoms is the most intuitive and reliable way to understand the reactions. However, experimentally observing the movement of atoms is extremely challenging. This is because the movement of atoms is 1) extremely subtle in terms of space and 2) very fast in terms of time. Therefore, to observe the movement of atoms, it is necessary to achieve high spatial and temporal resolution.
1) X-ray scattering: determining molecular structure
X-ray scattering can be utilized to experimentally observe the structure of molecules, specifically the positions of atoms that compose the molecule. X-ray scattering signals are a function of the distances between atoms. As depicted in the diagram below, when the distance between two atoms increases, the peaks in the scattering signal appear more densely, whereas when the distance between two atoms decreases, the peaks in the scattering signal become more dispersed. Ultimately, by experimentally obtaining and analyzing X-ray scattering signals, the structure of molecules can be determined. X-ray scattering signals are sensitive even to atomic movements at the Angstrom scale, enabling precise measurement of structural changes in reacting molecules.
X-ray scattering signal is sensitive to distances between atoms. Thus, 3D molecular structure can be determined based on the X-ray scattering signal.
2) Pulsed light source: capturing time-dependent structural change
To track the time-dependent structural changes of molecules, a high temporal resolution is required. To capture the trajectory of a moving object with a high-speed camera, the camera's shutter is opened for a short period of time, allowing light to pass through for only a brief duration.
Similarly, by probing the molecule with X-ray light for an extremely short period of time, the movement of atoms can be captured. However, as atomic movements occur at the femtosecond timescale, the X-ray light should have a duration in the femtosecond timescale. The light in the form of an extremely short duration is called a pulse.
Pulsed X-ray light can be obtained from accelerator facilities. In particular, with an X-ray free-electron laser (XFEL), which is the 4th generation accelerator, femtosecond X-ray pulses can be obtained. Consequently, by utilizing an X-ray pulse, it becomes possible to capture the instantaneous positions of rapidly moving atoms.
3) Capturing molecular motion: time-resolved X-ray scattering
Ultimately, by measuring X-ray scattering signals with femtosecond X-ray pulses from the molecule in action, the transient structure of the molecule can be determined. Furthermore, by probing the molecule with X-ray pulses at different time points from the initiation of the reaction, the structural changes of the molecule can be tracked in real-time. This allows for obtaining a kind of 'molecular movie' that reveals the dynamic structural changes.
Analyzing X-ray scattering patterns obtained during the progress of the reaction enables us to track the structural changes of the molecule, thereby visualizing the reaction in real space and real time.
This experimental technique is known as time-resolved X-ray scattering or time-resolved X-ray liquidography. It commonly involves the use of laser and X-ray pulses. A laser pulse can initiate a photoinduced reaction, and the resulting structural changes can be investigated by analyzing X-ray scattering signals at various time delays following the initiation of the reaction.
A schematic diagram illustrating a time-resolved X-ray scattering experiment. A laser pulse is employed to initiate a reaction, while an X-ray pulse is used to detect structural changes of the molecule.
Reaction Mechanism Study
Our group aims to visualize the structural change of molecules involved in chemical and biological reactions. If we can observe the structural changes of molecules and track the motion of atoms with time-resolved X-ray scattering, what can we ultimately achieve? Visualizing the temporal evolution of molecular structures during a reaction allows us to elucidate the reaction mechanism with clarity. Studying the reaction mechanism provides crucial information for understanding and controlling reactions, such as manipulating product selectivity, enhancing the efficiency of catalytic reactions, and targeting specific reaction intermediates to suppress undesired reactions. Our group aims to directly observe the structural changes of various inorganic/organic molecules. Recently, with the utilization of femtosecond X-ray pulses obtained from XFEL facilities, the temporal resolution of experiments has significantly improved. As a result, we have reached a level where we can directly observe the structures of molecular transition states and obtain experimental information about the potential energy surface. By visualizing the molecular structural changes, we will be able to unveil numerous hidden mysteries behind chemical and biological reactions.
Protein Structural Dynamics
Understanding the structural changes of proteins is crucial for unraveling various biological phenomena, as protein function is closely associated with its three-dimensional structure. By elucidating protein structural dynamics, we can provide essential information for understanding a wide range of life processes. Our research group aims to visualize the structural changes of proteins during reactions using time-resolved X-ray scattering. By employing X-ray scattering with high temporal and spatial resolution, we can investigate protein structure dynamics in physiological environments. However, due to the complexity of protein structures compared to small molecules, we need to utilize various computational techniques for analysis. In our group, we employ Monte Carlo simulations, Molecular Dynamics simulations, and machine learning to study protein structural dynamics. By visualizing protein structural changes, we anticipate shedding light on the understanding of diverse biological phenomena and the mechanisms underlying disease development.
Protein Kinetics & 3D Structure of Protein Intermediate
The analysis of time-resolved X-ray scattering data for a protein can unveil intricate protein kinetics and the three-dimensional structure of protein intermediates. Through kinetic and structural analyses, it is possible to elucidate the reaction mechanism of protein reactions and track specific tertiary and quaternary structural changes in real time.
