Every moment of ultrafast chemical bonding now captured on film
The emerging moment of bond formation, two separate bonding steps, and subsequent vibrational motions were visualized

Date:
June 24, 2020
Source:
Institute for Basic Science
Summary:
Scientists report the direct observation of the birthing moment
of chemical bonds by tracking real-time atomic positions in the
molecule.

They captured the ongoing reaction process of the chemical bond
formation in the gold trimer. The femtosecond-resolution images
revealed that such molecular events took place in two separate
stages, not simultaneously as previously assumed.



FULL STORY ========================================================================== Targeted cancer drugs work by striking a tight bond between cancer cell
and specific molecular targets that are involved in the growth and spread
of cancer. Detailed images of such 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 Institute of 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. "We finally succeeded in capturing the ongoing reaction process of the chemical bond formation in 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 gold trimer complex atoms remain in motion
even after the chemical bonding is complete. The distance between the
atoms increased and decreased periodically, exhibiting the molecular
vibration. These visualized molecular vibrations allowed us to name the characteristic motion of each observed vibrational mode." adds Ihee.

Atoms move extremely fast at a scale of femtosecond (fs) -- quadrillionths
(or millionths of a billionth) of a second. Its movement is minute
in the level of angstrom equal to one ten-billionth 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 made this 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 the chemical
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 to interrogate the bond-forming process.

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).

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 the molecule complex resulted in multiple characteristic
scattering images over time. When a molecule is excited by a laser pulse, multiple vibrational quantum states are simultaneously excited. The superposition of several excited vibrational quantum states is called
a wave packet. The researchers tracked the wave packet in three-
dimensional nuclear coordinates and found 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.

They also accurately illustrated molecular vibration motions in both
temporal- and spatial-wise. This is quite a remarkable feat considering
that such an ultrafast speed and a minute length 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. In this study, the progress of the bond formation and bent-to-linear structural transformation could be observed in real time,
thanks to the improvement 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 the bent-to-
linear transformation completed in 335 fs were visualized. 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 with dramatically improved experimental and analytical methods.

They will push this method of 'real-time tracking of atomic positions in
a molecule and molecular vibration using femtosecond x-ray scattering'
to reveal the mechanisms of organic and inorganic catalytic reactions and reactions involving proteins in the human body. "By directly tracking the molecular vibrations and real-time positions of all atoms in a molecule
in the middle of reaction, we will be able to uncover mechanisms of
various unknown organic and inorganic catalytic reactions and biochemical reactions," notes Dr. KIM Jong Goo, the first author of the study.


========================================================================== Story Source: Materials provided by Institute_for_Basic_Science. Note:
Content may be edited for style and length.


========================================================================== Journal Reference:
1. 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,
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. Mapping the
emergence of molecular vibrations mediating bond formation. Nature,
2020 DOI: 10.1038/s41586-020-2417-3 ==========================================================================

Link to news story: https://www.sciencedaily.com/releases/2020/06/200624120443.htm

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