Structure analysis of an reactive intermediate in organic solvent using X-ray

We have recentry reported a paper entitled "Lewis acid-mediated Suzuki–Miyaura cross-coupling reaction". In this study, I was in charge of XAS experiments and theoretical calculations, but there were many struggles before the paper was published. I would like to write about the process of my work.
Published in Chemistry
Structure analysis of an reactive intermediate in organic solvent using X-ray

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In the spring of 2019, I was at a synchrotron radiation facility in Tsukuba.

I was (and still am) a synthetic organic chemist. When I was a postdoctoral fellow at RIKEN, I worked on the development of reactions using transition-metal-catalysts. In my current position at Osaka Univ., I am engaged in the development of reactions using metal nanoparticles and the synthesis of sumanene (a bowl-shaped π-conjugated molecule) and related derivatives, but that is just to say that I am involved in a little wide range of research fields that it does not go beyond synthetic organic chemistry. To be honest, I was confused. It was a bolt from the blue. 

In fact, there are not many spectroscopic methods required for synthetic organic chemistry, and if you can use NMR and MS machines, you can carry out your research even if you don't understand the principles of spectroscopy. In recent years, it is not necessary to submit infrared absorption spectroscopy data when submitting a paper, and in fact I was also not familiar with spectroscopic measurements at the time. Although I had never even measured UV-vis spectroscopic before, I had to start working on X-ray absorption spectroscopy (XAS) at the synchrotron radiation facility, following my revelation. For a year, I was plagued by incomprehensible waves.


When I started to understand the meaning of XAS (a year passed without any fruitful spectroscopic data), I realized that the technique could provide information that is difficult to obtain by other analytical methods in the analysis of reaction mechanism of homogeneous metal-catalysed reaction. XAS consists of two regions called XANES and EXAFS. XANES provides information on the electronic state and the structure of ligand field of the element of interest. Meanwhile, EXAFS provides information of the type, interatomic distances, and coordination numbers of elements located in the vicinity of the target element. Since one of the advantages of XAS is the high elemental selectivity due to the wide energy range required to excite the inner-shell electrons, however, for me, the ability to obtain spectra in solution was very attractive because there are few known experimental methods for obtaining structural and electronic information in organic solvents. And so it goes, I started a collaborative work with my former vice-boss, Dr. Takashi Niwa, but soon realised that it was not easy and I hit another big wall:

Liquid cells for XAS experiment are not commercially available!

It is commonplace for researchers in such research facilities to manufacture their own cells and instrumentations, and they have a lot of unique know-how. However, there is not much information available to the public, which is an extremely high barrier for beginners. In addition, the use of organic solvents is also a problem, and it is necessary to use materials that do not deteriorate in organic solvents to manufacture a liquid cell (Pic. 1). In such a situation, the person who helped me was the boss of the current position, Prof. Hidehiro Sakurai. He is well-connected and kindly introduced me to Prof. Hikaru Takaya, who is the most active researcher in XAS analysis on homogeneous catalysis in Japan. Coincidentally, our beam time at SPring-8 BL14B2 was around the same time, so I was able to have a direct discussion with him. I believe that this was definitely a major turning point for this project.

Pic. 1. Making a liquid cell with a drilling machine (left). Scene of solution XAS experiment at SPring-8 (right). 


It was also my first attempt to elucidate the mechanism using theoretical calculations. In this regard, I am very grateful to Dr. Hiroaki Iwamoto, a former colleague at Osaka Univ. He is a specialist in reaction development and computational chemistry in transition-metal-catalysis and was kind enough to share with me his knowledge of computational chemistry and how to correctly interpret the results. I shared the knowledge with Dr. Takashi, and through careful investigation, we were able to gain a deeper understanding of the reaction mechanism.


Finally, this joint research was made satisfactory by various coincidences and encounters with many researchers. Additionally, I am honored that our art was chosen for the cover of Nature Catalysis (Volume 4 Issue 12, December 2021). The projector in the centre was inspired by the architecture of a synchrotron radiation facility, and the light balls represent charged particles orbiting in a storage ring.

For more information, please read our paper in Nature Catalysis. “Lewis acid-mediated Suzuki–Miyaura cross-coupling reaction”

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