Computational analysis of the spatial distributions of low-energy electrons generated via water photolysis and photoinjection into electrodes in water

Kai, Takeshi; Toigawa, Tomohiro; Matsuya, Yusuke*; Hirata, Yuho; Tsuchida, Hidetsugu*; Yokoya, Akinari*

Journal of Chemical Physics, 162(15), p.154102_1 - 154102_11, 2025/04

https://doi.org/10.1063/5.0252783

Scientific knowledge of low-energy electrons resulting from water radiolysis is required to estimate radiation DNA damage. However, since the analysis of water radiolysis is very complex, this study focuses on the experimental values of low-energy electrons related to simple water photolysis and those generated by photoirradiation of electrodes in water. Both experimental analyses involve the presence or absence of a Coulomb field in the parent ion. In this study, we analyzed these experimental values using a calculation code that combines Monte Carlo and molecular dynamics methods. As a result, it was shown that the code reproduced the experimental values even under different experimental conditions, and the code was validated. The calculation code will be a powerful tool for analyzing the interaction between low-energy electrons and DNA, and is expected to be applied to elucidate the formation mechanism of radiation DNA damage.

Significant role of secondary electrons in the formation of a multi-body chemical species spur produced by water radiolysis

Kai, Takeshi; Toigawa, Tomohiro; Matsuya, Yusuke*; Hirata, Yuho; Tezuka, Tomoya*; Tsuchida, Hidetsugu*; Yokoya, Akinari*

Scientific Reports (Internet), 14, p.24722_1 - 24722_15, 2024/10

https://doi.org/10.1038/s41598-024-76481-z

Scientific insight of water radiolysis is essential to estimate the direct and indirect effects of radiation DNA damage. Secondary electrons produced by water radiolysis are responsible for both effects. Here, we use a first-principles code to calculate the femtosecond dynamics of secondary electrons produced as a result of 20-30 eV energy deposition to water and analyze the formation mechanism of radiolytic chemical species produced in a nano-size ultra-small space region. From the results, it was clarified that the chemical species produced by water radiolysis begin to densify in the ultra-small region of a few nanometers when the deposition energy exceeds 25 eV. Our results provide important scientific insights into the formation of clustered DNA damage, which is believed to cause biological effects such as cell death.

Consideration of the dielectric response for radiation chemistry simulations

Toigawa, Tomohiro; Kai, Takeshi; Kumagai, Yuta; Yokoya, Akinari*

Journal of Chemical Physics, 160(21), p.214119_1 - 214119_9, 2024/06

https://doi.org/10.1063/5.0211089

The spur reaction is crucial for determining radiolysis or photolysis in liquid, but the spur expansion process has yet to be elucidated. One reason is the need to understand the role of the dielectric response of the solvating molecules surrounding the charged species generated by ionization. The dielectric response corresponds to the time evolution of the permittivity and might affect the chemical reaction-diffusion of the species in a spur expansion process. This study examined the competitive relationship between reaction-diffusion kinetics and the dielectric response by solving the Debye-Smoluchowski equation while considering the dielectric response. The Coulomb force between the charged species gradually decreases with the dielectric response. Our calculation results found a condition where fast recombination occurs before the dielectric response is complete. Although it has been reported that the primary G-values of free electrons depend on the static dielectric constant under low-linear-energy transfer radiation-induced ionization, we propose that considering the dielectric response can provide a deeper insight into fast recombination reactions under high-linear-energy transfer radiation- or photo-induced ionization. Our simulation method enables the understanding of fast radiation-induced phenomena in liquids.

Incorporation of a bromine atom into DNA-related molecules changes their electronic properties

Hirato, Misaki*; Yokoya, Akinari*; Baba, Yuji*; Mori, Seiji*; Fujii, Kentaro*; Wada, Shinichi*; Izumi, Yudai*; Haga, Yoshinori

Physical Chemistry Chemical Physics, 25(21), p.14836 - 14847, 2023/05

https://doi.org/10.1039/D3CP01597A

Initial yield of hydrated electron production from water radiolysis based on first-principles calculation

Kai, Takeshi; Toigawa, Tomohiro; Matsuya, Yusuke*; Hirata, Yuho; Tezuka, Tomoya*; Tsuchida, Hidetsugu*; Yokoya, Akinari*

RSC Advances (Internet), 13(11), p.7076 - 7086, 2023/03

https://doi.org/10.1039/D2RA07274B

Scientific insights of water radiolysis are widely used in the life sciences and so on, however, the formation mechanism of radicals, a product of water radiolysis, is still not well understood. We are challenging to develop a simulation code to solve this formation mechanism from the viewpoint of radiation physics. Our first-principles calculations have revealed that the behavior of secondary electrons in water is governed not only by collisional effects but also by polarization effects. Furthermore, from the predicted ratio of ionization to electronic excitation, based on the spatial distribution of secondary electrons, we successfully reproduce the initial yield of hydrated electrons predicted in terms of radiation chemistry. The code provides us a reasonable spatiotemporal connection from radiation physics to radiation chemistry. Our findings are expected to provide newly scientific insights for understanding the earliest stages of water radiolysis.

Dense radical formation in L-alanine-3,3,3-d3 and L-alanine-d4 by 1.5 keV soft X-ray irradiation

Nakagawa, Seiko*; Oka, Toshitaka; Fujii, Kentaro*; Yokoya, Akinari*

Radiation Physics and Chemistry, 192, p.109884_1 - 109884_5, 2022/03

https://doi.org/10.1016/j.radphyschem.2021.109884

Radicals produced in crystalline L-alanine-3,3,3-d3 and L-alanine-d4 were observed by the electron spin resonance (ESR) technique during 1.5 keV soft X-ray irradiation. The line width of the ESR spectra obtained by the soft X-ray irradiation was 1.5 times wider than that of hard X-rays from a previous report, meaning a higher density of radicals. The efficiency of the radical yield by the soft X-ray irradiation was 10 relative to that by -irradiation. For the soft X-ray irradiation, many radicals will be lost by the efficient radical-radical recombination due to the higher density of the radicals, just as the high-LET irradiation by heavy ions. We concluded that the high LET nature of the lower energy photons leads to the dense radical formation in the crystalline alanine powder.

A Significant role of non-thermal equilibrated electrons in the formation of deleterious complex DNA damage

Kai, Takeshi; Yokoya, Akinari*; Ukai, Masatoshi*; Fujii, Kentaro*; Toigawa, Tomohiro; Watanabe, Ritsuko*

Physical Chemistry Chemical Physics, 20(4), p.2838 - 2844, 2018/01

https://doi.org/10.1039/C7CP06903K

It is thought that complex DNA damage which induces in radiation biological effects is formed at radiation track end. Thus, the earliest stage of water radiolysis at the electron track end was studied to predict DNA damage. These results indicate that DNA damage sites comprising multiple nucleobase lesions with a single strand breaks can therefore be formed by multiple collisions of the electrons within three base pairs (3bp) of a DNA strand. This multiple damage site cannot be processed by base excision repair enzymes. However, pre-hydrated electrons can also be produced resulting in an additional base lesion more than 3bp away from the multi-damage site. This clustered damage site may be finally converted into a double strand break (DSB) when base excision enzymes process the additional base lesions. These DSBs include another base lesion(s) at their termini that escape from the base excision process and which may result in biological effects such as mutation in surviving cells.

Dynamic behavior of secondary electrons produced by a high-energy electron in liquid water

Kai, Takeshi; Yokoya, Akinari*; Fujii, Kentaro*; Watanabe, Ritsuko*

Yodenshi Kagaku, (8), p.11 - 17, 2017/03

It is thought to that the biological effects such as cell death or mutation are induced by complex DNA damage which are formed by several damage sites within a few nm. We calculated dynamic behavior of secondary electrons produced by primary electron and positon of high energy in water whose composition ratio is similar to biological context. The secondary electrons induce the ionization or electronic excitation near the parent cations. The decelerated electrons about 10% are distributed to their parent cations by the attractive Coulombic force. From the results, we predicted the following formation mechanism for the complex DNA damage. The electrons ejected from DNA could induce the ionization or the electronic excitation within the DNA. The electrons attracted by the Coulombic force are pre-hydrated in water layer of the DNA. The pre-hydrated electrons could induce to the DNA damage by dissociative electron transfer. As the results, the complex DNA damage with 1 nm could be formed by the interaction of not only the primary electron or positon but also the secondary electrons.

Dynamic behavior of secondary electrons in liquid water at the earliest stage upon irradiation; Implications for DNA damage localization mechanism

Kai, Takeshi; Yokoya, Akinari*; Ukai, Masatoshi*; Fujii, Kentaro*; Watanabe, Ritsuko*

Journal of Physical Chemistry A, 120(42), p.8228 - 8233, 2016/10

https://doi.org/10.1021/acs.jpca.6b05929

Low energy secondary electrons produced by an ionizing radiation in a living cell may involve in formation of complexed DNA damage. We performed theoretical study for numerical calculation of dynamic behavior of the electrons to imply a formation of radiation damage to DNA. The decelerating electrons are gradually attracted to their parent cations by the Coulombic force within hundreds of fs, and about 12.6 % of electrons are finally distributed within 2 nm from the cations. The collision fraction of the ionization and excitation within 1 nm from the cation was estimated to be about 40 %. From those analyses, we suggested a process of DNA damage that the secondary electrons may cause highly localized lesions around a cation in DNA molecule through additional dissociative electron transfer as well as the ionization or the excitation if the electrons are ejected from DNA. The localized damage may involve ultimately in biological effects such as cell death or mutation induction.

Ultraviolet circular dichroism spectroscopy for protein structural study

Izumi, Yudai; Yamamoto, Satoshi*; Fujii, Kentaro; Yokoya, Akinari

Hoshasen Seibutsu Kenkyu, 51(1), p.91 - 106, 2016/03

no abstracts in English