XFEL diffraction reveals hydrogen atoms in small organic crystals

A recent breakthrough by an all-RIKEN team has showcased the power of extremely intense X-ray pulses in pinpointing hydrogen atom positions within small organic molecule crystals. This advancement holds significant promise for fields like drug discovery and materials research.

Since the groundbreaking work of William Lawrence Bragg and his father, William Henry Bragg, who demonstrated the distinct patterns produced by X-rays scattered from crystals a century ago, X-ray diffraction has been the leading technique for revealing crystalline material structures. However, many materials form minuscule crystals that defy analysis through X-ray diffraction.

Koji Yonekura from RIKEN SPring-8 Center emphasizes, “Analyzing structures of small crystals is vital in areas like synthetic organic chemistry, pharmaceutical science, and materials science, especially when larger crystals aren’t feasible.”

Shifting from X-rays to electrons could enable the study of smaller crystals, but this method demands exceptionally thin samples. Another avenue of promise lies in ultra-intense, ultrashort X-ray pulses generated by X-ray free electron lasers (XFELs), sprawling facilities spanning kilometers.

In a significant achievement, Kiyofumi Takaba, Saori Maki-Yonekura, and their collaborators harnessed XFEL-generated X-rays to unravel the structure of a minute organic molecule, the fluorescent dye rhodamine-6G. They also contrasted their findings with those from 3D electron diffraction for the same molecule.

The researchers managed to discern hydrogen atom positions using both techniques—an impressive feat given hydrogen’s minute size, consisting solely of a proton and electron. These positions depended on the bonds connecting hydrogen atoms. Their findings, published in Nature Chemistry, mark the first-ever visualization of hydrogen atoms in small organic crystal structures through XFEL diffraction.

Takaba highlights the significance, stating, “This achievement is crucial since a hydrogen atom’s position unveils chemical bond polarity, which greatly influences the properties and functions of organic molecules.”

While the molecular structures deduced from the two methods closely resembled each other, they provided complementary insights due to the distinct interactions of electrons and X-rays with the samples. “XFEL and electron crystallography unveil diverse and detailed aspects of organic compounds,” notes Maki-Yonekura. XFEL excelled in more accurate atomic coordinate determination, whereas electron diffraction sensitively captured the molecule’s electric charge distribution.

Significantly, neither technique necessitated specialized sample preparation, enhancing their practicality.

The team’s future endeavors involve further investigating how specimens interact with various probes. Takaba anticipates, “We anticipate extending the applications of these techniques and advancing our theoretical comprehension of the methods themselves.”

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