Nano/Bio Structural Dynamics Lab.

One of the most fundamental questions in biology, chemistry, and physics is how the molecules interact, so called, reaction mechanisms. Our laboratory strives to understand the reaction mechanisms in molecular detail in gas phase, solution phase, and solid phase spanning amorphous phase, polycrystalline and single crystals. Traditionally, femtosecond spectroscopy has been used to achieve this goal, however, spectroscopic data, in most cases, fail to provide direct information on the structural changes such as bond lengths and bond angles. To remedy this, we combine the traditional femtoscience with direct structural tools such as diffraction, EXAFS, and NMR. These techniques can be applied to a wide range of systems, encompassing small molecules, nano-scale complexes, and macromolecules such as polymers, proteins and DNA. A typical experiment is conducted in a pump-probe manner; an optical pulse such as femtosecond laser pulse is directed to the sample of interest to initiate a desired reaction, and after a well-defined time delay, a probing pulse such as an ultrashort x-ray pulse is sent to the sample undergoing a reaction. Then, the signal resulted from the interaction of the reacting system and the probing pulse captures the molecular actions in real time. Since the measured signal (in this case, diffraction signal) is a function of molecular structures, the time-dependant data at various time delays contains a clue to the molecular reaction mechanisms and a novel data analysis of the time-resolved signal finally reveals the mechanism.

Protein Structural Dynamics: Time-Resolved X-ray Crystallography

Our laboratory is interested in the reaction mechanisms of various proteins such as a blue light photoreceptor, bacteriorhodopsin, phytochrome, and LOV2 domain. These proteins play indispensible roles in the signal transduction pathway of a cellular system. The time-resolved X-ray Laue diffraction on a single crystal is currently the only method which can provide us detailed real-time structural information in sub-nanosecond time resolution at room temperature.The experiment is conducted at a third generation synchrotron facility such as ESRF and APS as the time-resolved X-ray liquid experiment. The difference is that the long-range order found in a single crystal enhances the diffraction signal and reduce the background significantly. Diffuse signal from disordered molecules becomes sharp peaks. Generally, a ns or fs laser pulse triggers the protein dynamics in a single crystal of proteins and a polychromatic, ultrashort X-ray pulse from a beamline of a synchrotron radiation facility sweeps through the single crystal. The resulting diffraction pattern is then recorded in a charge-coupled device (CCD) based detection system. Typically a better time resolution can be achieved when the single crystal is kept still and a polychromatic X-ray beam is used for diffraction unlike a traditional X-ray crystallographic experiment where a diffraction pattern of a monochromatic X-ray beam is measured on an oscillating crystal. However, our laboratory is also developing a new technique of achieving a better time resolution with the traditional monochromatic X-ray pulses so that a wider range of protein reactions can be studied.

Molecular Dynamics of Small Molecules, Nano-Scale Molecules and Macromolecules in Solution: Time-Resolved X-ray Liquid Diffraction

Third-generation synchrotron radiation facility such as European Synchrotron Radiation Facility (ESRF) and Advanced Photon Source (APS) can generate an X-ray pulse as short as 100 picoseconds (ps, 10-12). Our laboratory conducts time-resolved experiments by utilizing such an ultrashort X-ray pulse as a probe. Of great interest is the molecular structure of short-lived intermediates and solute-solvent interactions in solution phase. X-ray has a much longer penetration depth than electron does, and this characteristic makes X-ray suited for solution studies. Although the current time resolution is generally behind that of time-resolved electron diffraction, a future X-ray source based on free electron laser technology will realize femtosecond (fs, 10-12) time resolution, opening up a new possibility of capturing the movement of molecules in real time. So far, a series of successful time-resolved X-ray diffraction experiments have been conducted on reactions of various small molecules and we are currently expanding this technique to study macromolecules such as nano-scale complexes and proteins.

Ab-Initio and DFT Quantum Chemical Calculation and Molecular Dynamics Simulation

Modern scientific advances have confirmed that experiments alone cannot provide a full story and convincing explanations on complex reaction mechanisms. Therefore, all our experimental endeavors accompany theoretical calculations including both ab-initio and DFT quantum chemical calculations and molecular dynamics simulations. Selected examples are molecular structures of short-lived intermediates, the photo-reaction of solute molecules in solution, and reaction pathway of proteins.

Time-Resolved Electron Diffraction

With the advance of fs laser technology and electron gun design, the time resolution of ultrafast electron diffraction has reached near 1 ps. This impressive time resolution has enabled us to capture the molecular structure of short-lived intermediates. However, the fundamental bond-making and bond-breaking processes occur in femtosecond regime, which is beyond the current technology. Our laboratory is developing a next-generation ultrafast electron diffraction technique, which is femtosecond electron diffraction (FED). This new technique is based on a light-driven RF electron gun producing a near-relativistic electron pulse. Upon realization of this new technique, a molecular vibration will be directly captured, fulfilling one of chemists' dreams.