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Publication Information- Paper Title: Mapping the emergence of molecular vibrations mediating bond formation- Journal, Publication Date: Nature, June 24, 2020 15:00 GMT (online) / June 25, 2020 (print issue)- Authors:
Jong Goo Kim, Shunsuke Nozawa, Hanui Kim, Eun Hyuk Choi, Tokushi Sato, Tae Wu Kim, Kyung Hwan Kim,
Hosung Ki, Jungmin Kim, Minseo Choi, Yunbeom Lee, Jun Heo, Key Young Oang, Kouhei Ichiyanagi, RyoFukaya, Jae Hyuk Lee, Jaeku Park, Intae Eom, Sae Hwan Chun, Sunam Kim, Minseok Kim, Tetsuo Katayama,
Tadashi Togashi, Sigeki Owada, Makina Yabashi, Sang Jin Lee, Seonggon Lee, Chi Woo Ahn, Doo-Sik Ahn,Jiwon Moon, Seungjoo Choi, Joonghan Kim, Taiha Joo, Jeongho Kim, Shin-ichi Adachi, and Hyotcherl Ihee*- DOI: 10.1038/s41586-020-2417-3- Contact Regarding this Press Release: Prof. Hyotcherl Ihee (hyotcherl.ihee@kaist.ac.kr), Mr. Daewoong
Bae, Head of IBS Communications Team (+82-42-878-8195, woongs@ibs.re.kr); or Ms. Dahee Carol Kim,Public Information Officer of IBS & Science Communicator (+82-42-878-8133, clitie620@ibs.re.kr), Public
Relations Office of KAIST (+82-42-350-2296, namsejin@kaist.ac.kr), Public Relations Office of KEK (+81-29879-6046, press@kek.jp), Public Relations Office of PAL (+82-54-279-1553, pjun@postech.ac.kr), Public
Relations Office of RIKEN (ex-press@riken.jp), JASRI (+81-791-58-2785, kouhou@spring8.or.jp)

Institute for Basic Science (IBS)
Korea Advanced Institute of Science and Technology (KAIST)High Energy Accelerator Research Organization (KEK)
Pohang Accelerator Laboratory (PAL)
RIKEN
Japan Synchrotron Radiation Research Institute (JASRI)

Every moment of ultrafast chemical bonding
now captured on film
The emerging moment of bond formation, two separate
bonding steps, and subsequent vibrational motions werevisualized.
Targeted cancer drugs work by striking a tight bond between cancer cell and specificmolecular targets that are involved in the growth and spread of cancer. Detailed images ofsuch chemical bonding sites or pathways can provide key information necessary for
maximizing the efficacy of oncogene treatments. However, atomic movements in a moleculehave never been captured in the middle of the action, not even for an extremely simple
molecule such as a triatomic molecule, made of only three atoms.
A research team led by IHEE Hyotcherl of the Institute for Basic Science (IBS, South Korea)(Professor, Department of Chemistry, KAIST), in collaboration with scientists at the Instituteof Materials Structure Science of KEK (KEK IMSS, Japan), RIKEN (Japan) and Pohang
Accelerator Laboratory (PAL, South Korea), reported the direct observation of the birthing
moment of chemical bonds by tracking real-time atomic positions in the molecule. “Wefinally succeeded in capturing the ongoing reaction process of the chemical bond formationin the gold trimer. The femtosecond-resolution images revealed that such molecular events
took place in two separate stages, not simultaneously as previously assumed,” says Associate
Director IHEE Hyotcherl, the corresponding author of the study. “The atoms in the goldtrimer complex atoms remain in motion even after the chemical bonding is complete. The
distance between the atoms increased and decreased periodically, exhibiting the molecularvibration. These visualized molecular vibrations allowed us to name the characteristic motionof each observed vibrational mode.” adds Ihee.

Figure 1. A schematic of the femtosecond x-ray scattering technique. The bond formation
reaction in a gold trimer complex is initiated by a laser pulse, and a three-dimensional
structure after a certain time delay is detected by an x-ray scattering image. (Credit: IBS)

Atoms move extremely fast at a scale of femtosecond (fs) — quadrillionths (or millionths ofa billionth) of a second. Its movement is minute in the level of angstrom equal to one tenbillionth of a meter. They are especially elusive during the transition state where reaction
intermediates are transitioning from reactants to products in a flash. The research team madethis experimentally challenging task possible by using femtosecond x-ray liquidography(solution scattering). This experimental technique combines laser photolysis and x-ray

scattering techniques. When a laser pulse strikes the sample, X-rays scatter and initiate thechemical bond formation reaction in the gold trimer complex. Femtosecond x-ray pulses
obtained from a special light source called an x-ray free-electron laser (XFEL) were used tointerrogate the bond-forming process. (Figure 1) The experiments were performed at two
XFEL facilities (4th generation linear accelerator), PAL-XFEL in South Korea and SACLA
in Japan, and this study was conducted in collaboration with researchers from KEK IMSS,
Pohang Accelerator Laboratory (PAL), RIKEN, and the Japan Synchrotron Radiation
Research Institute (JASRI).

Figure 2. (left) Time-dependent positions of the wave packet in the multidimensional nuclear
coordinates were obtained from the femtosecond x-ray scattering experiment on a goldtrimer complex. (Credit: Nature & IBS)
(right) By inspecting the motion of the wave packet, it was revealed that the bond formation
reaction in the gold trimer complex occurs through an asynchronous bond formation
mechanism. (Yellow: gold atoms, gray: carbon atom, blue: nitrogen atom, 1000 times 1 fs is
1 picosecond (ps), 1000 times 1 ps is 1 nanosecond (ns)) (Credit: KEK IMSS)

Movie: Emergence of molecular vibrations and the evolution to covalent bonds observed inthis research. (Credit: KEK IMSS)（URL: https://youtu.be/e8-vdKTD8cY）
The movement of three gold atoms measured in this study is shown on the upper left. At 0 fs,the sample was excited by UV light. The table on the upper right shows the measured valuesof the molecular structure during the photochemical reaction. The horizontal and verticalaxes of the 2D graph on the lower left are the distances between gold atoms A-B and B-C,respectively. In the 2D graph, the points represented by S0 and T1’ correspond to themolecular structures before the photochemical reaction and after linear transformation during
the reaction process, respectively. The molecular structure changed from S0 to T1’ along thered line known as a “reaction path”. The 3D graph shown in the lower right was made byadding an energy axis to the 2D graph. The curved surface drawn in the 3D graph is known
as a "potential energy surface (PES)". The photochemical reaction is described by themovement of the corresponding position in the 3D graph, and the reaction path can beexpected to connect the valleys of the PES. Before UV light excitation, the correspondingposition is at the bottom of the PES of S0. When a molecule is excited by UV light, theenergy of the molecule is increased, but the molecular structure is still maintained. Therefore,
the corresponding position moves vertically in the 3D graph. Then, the molecule structure
begins to change with a decrease of its energy, and the corresponding position slides down
the PES of T1' along the valley. Finally, the molecular structure becomes linear, and thecorresponding position reaches the bottom of the PES of T1'. Until now, to calculate thereaction path, the structural change during a chemical reaction has been discussed.
However, in this research, we are able to determine the reaction path without relying on acalculation.

Scattered waves from each atom interfere with each other and thus their x-ray scattering
images are characterized by specific travel directions. The IBS research team traced real-time
positions of the three gold atoms over time by analyzing x-ray scattering images, which aredetermined by a three-dimensional structure of a molecule. Structural changes in themolecule complex resulted in multiple characteristic scattering images over time. When amolecule is excited by a laser pulse, multiple vibrational quantum states are simultaneouslyexcited. The superposition of several excited vibrational quantum states is called a wave
packet. The researchers tracked the wave packet in three-dimensional nuclear coordinates andfound that the first half round of chemical bonding was formed within 35 fs after
photoexcitation. The second half of the reaction followed within 360 fs to complete the entire
reaction dynamics. (Figure 2)
They also accurately illustrated molecular vibration motions in both temporal- and spatialwise. This is quite a remarkable feat considering that such an ultrafast speed and a minutelength of motion are quite challenging conditions for acquiring precise experimental data.
In this study, the IBS research team improved upon their 2015 study published by Nature. In
the previous study in 2015, the speed of the x-ray camera (time resolution) was limited to 500
fs, and the molecular structure had already changed to be linear with two chemical bonds
within 500 fs. (Figure 2, upper right) In this study, the progress of the bond formation andbent-to-linear structural transformation could be observed in real time, thanks to theimprovement time resolution down to 100 fs. Thereby, the asynchronous bond formation
mechanism in which two chemical bonds are formed in 35 fs and 360 fs, respectively, and thebent-to-linear transformation completed in 335 fs were visualized. (Figure 2, lower right) In
short, in addition to observing the beginning and end of chemical reactions, they reported
every moment of the intermediate, ongoing rearrangement of nuclear configurations withdramatically improved experimental and analytical methods.
They will push this method of 'real-time tracking of atomic positions in a molecule andmolecular vibration using femtosecond x-ray scattering’ to reveal the mechanisms of organicand inorganic catalytic reactions and reactions involving proteins in the human body. “Bydirectly tracking the molecular vibrations and real-time positions of all atoms in a molecule inthe middle of reaction, we will be able to uncover mechanisms of various unknown organicand inorganic catalytic reactions and biochemical reactions,” notes Dr. KIM Jong Goo, thefirst author of the study.

Notes for editors- References
Mapping the emergence of molecular vibrations mediating bond formation. Jong Goo Kim,Shunsuke Nozawa, Hanui Kim, Eun Hyuk Choi, Tokushi Sato, Tae Wu Kim, Kyung HwanKim, Hosung Ki, Jungmin Kim, Minseo Choi, Yunbeom Lee, Jun Heo, Key Young Oang,Kouhei Ichiyanagi, Ryo Fukaya, Jae Hyuk Lee, Jaeku Park, Intae Eom, Sae Hwan Chun,Sunam Kim, Minseok Kim, Tetsuo Katayama, Tadashi Togashi, Sigeki Owada, Makina
Yabashi, Sang Jin Lee, Seonggon Lee, Chi Woo Ahn, Doo-Sik Ahn, Jiwon Moon, Seungjoo

Choi, Joonghan Kim, Taiha Joo, Jeongho Kim, Shin-ichi Adachi, and Hyotcherl Ihee*.
Nature. DOI: 10.1038/s41586-020-2417-3- About the Institute for Basic Science (IBS)IBS was founded in 2011 by the government of the Republic of Korea with the sole purposeof driving forward the development of basic science in South Korea. IBS has 30 research
centers as of January 2020. There are ten physics, two mathematics, six chemistry, six life
science, one Earth science, and five interdisciplinary research centers.
https://www.ibs.re.kr/eng.do- About Korea Advanced Institute of Science and Technology (KAIST)KAIST is the first and top science and technology university in Korea. KAIST was foundedby the Korean government in 1971 as the nation’s first research-oriented science andengineering institution.
https://www.kaist.ac.kr/en/- About High Energy Accelerator Research Organization (KEK)KEK was established to promote various types of researches as a center of excellence foroverall development of Japan’s accelerator science (particle and nuclear research using highenergy accelerators, research on the structure/function of matter including living organisms,
research on improving the accelerator performance, and related basic technologies). As theInter‐University Research Institute Corporation, KEK provides researchers across the countryand abroad with opportunities for research. With the Tsukuba and Tokai campuses as centers
for excellence, KEK joins international collaboration experiments and developments.
In addition, KEK is in charge of the School of High Energy Accelerator Science of theGraduate University for Advanced Studies (SOKENDAI).
https://www.kek.jp/en/- About Pohang Accelerator Laboratory (PAL)
PAL is an affiliated research institute of Pohang university of science and technology,
founded in 1988. PAL operates Pohang Light Source (PLS), a synchrotron radiation facility,and PAL-XFEL, an x-ray free-electron laser.
http://pal.postech.ac.kr/paleng/- About RIKEN
RIKEN is Japan's largest comprehensive research institution renowned for high-quality
research in a diverse range of scientific disciplines. Founded in 1917 as a private researchfoundation in Tokyo, RIKEN has grown rapidly in size and scope, today encompassing anetwork of world-class research centers and institutes across Japan.
https://www.riken.jp/en/- About Japan Synchrotron Radiation Research Institute (JASRI)JASRI is a public interest incorporated foundation in charge of the operation, maintenance,management, and provision of support for users of the SPring-8 synchrotron radiation

facility, as well as the provision of support for users of the X-ray free electron laser SACLA.
JASRI is a highly professional, advanced, interdisciplinary, and international institute.
(SPring-8/SACLA http://www.spring8.or.jp/en/, JASRI http://www.jasri.jp/en/index.html)