Nature of the physicochemical process in water photolysis uncovered by a computer simulation

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

Journal of Chemical Physics, 158(16), p.164103_1 - 164103_8, 2023/04

New insight into water radiolysis and photolysis is indispensable in the dramatic progress of sciences and technologies in various research areas. In the radiation field, reactive hydrated electrons are considerably produced along radiation tracks. Although the formation results from a transient dynamic correlation between ejected electrons and water, the individual mechanisms of electron thermalization, delocalization, and polarization are unknown. Using a dynamic Monte Carlo code, we show herein that the ejected electrons are immediately delocalized by molecular excitations in parallel with phonon polarization and gradually thermalized by momentum transfer with an orientation polarization in a simultaneous manner. Our results show that these mechanisms heavily depend on the intermolecular vibration and rotation modes peculiar to water. We expect our approach to be a powerful technique for connecting physical and chemical processes in various solvents.

Deceleration processes of secondary electrons produced by a high-energy Auger electron in a biological context

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

International Journal of Radiation Biology, 92(11), p.654 - 659, 2016/11

https://doi.org/10.1080/09553002.2016.1195933

Thermal equilibrium and prehydration processes of electrons injected into liquid water calculated by dynamic Monte Carlo method

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

Radiation Physics and Chemistry, 115, p.1 - 5, 2015/10

https://doi.org/10.1016/j.radphyschem.2015.05.021

Role of secondary electrons on DNA damage have not been understood sufficiently because there still exists a lack of study for thermalization process of an electron in liquid phase. We calculated thermalization lengths and spatial distributions of an electron in liquid water using cross sections for rotation and phonon excitations in a liquid phase. Obtained thermalization lengths are in good agreement with experimental results reported by literatures. Thermalization time was also estimated from time evolution of spatial distributions of the incident electron to be hundreds femtoseconds. From these results, we predict that thermalization and pre-hydration of electron might progress simultaneously. These electrons possibly cause damage in biological molecules in a cell. Particularly severe types of DNA damage consisting of proximately located multiple lesions are potentially induced by reaction of DNA with the thermalized electrons by dissociative electron transfer.

Cross sections, stopping powers, and energy loss rates for rotational and phonon excitation processes in liquid water by electron impact

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

Radiation Physics and Chemistry, 108, p.13 - 17, 2015/03

https://doi.org/10.1016/j.radphyschem.2014.11.008

Role of secondary electrons on DNA damage have not been understood sufficiently because there still exists a lack of cross section of rotational and phonon excitation in the liquid phase for precise simulation of the electron behavior. We calculated cross sections, stopping powers, and energy loss rates for the excitations in liquid water. The values for rotation are less by three orders of magnitude than those in the gas phase, while the values for phonon are close to those reported for amorphous ice. Thermalization process has so far been estimated from an assumption that the energy loss rates do not depend strongly on the energy below 1 eV. However, we found that the energy loss rates depend significantly on the energy. This fact indicates that the thermalization time will be longer than the previously estimated time, and we predict that thermalization process strongly involve in subsequent hydrated and chemical processes. The data set provide here is expected to useful to make the role of the secondary electrons on DNA damage much clear.

Nitrogen K-edge X-ray absorption near edge structure (XANES) spectra of purine-containing nucleotides in aqueous solution

Shimada, Hiroyuki*; Fukao, Taishi*; Minami, Hirotake*; Ukai, Masatoshi*; Fujii, Kentaro; Yokoya, Akinari; Fukuda, Yoshihiro*; Saito, Yuji

Journal of Chemical Physics, 141(5), p.055102_1 - 055102_8, 2014/08

https://doi.org/10.1063/1.4891480

Structural changes of nucleic acid base in aqueous solution as observed in X-ray absorption near edge structure (XANES)

Shimada, Hiroyuki*; Fukao, Taishi*; Minami, Hirotake*; Ukai, Masatoshi*; Fujii, Kentaro; Yokoya, Akinari; Fukuda, Yoshihiro*; Saito, Yuji

Chemical Physics Letters, 591, p.137 - 141, 2014/01

https://doi.org/10.1016/j.cplett.2013.11.026

Spectroscopic study of radiation-induced DNA lesions and their susceptibility to enzymatic repair

Yokoya, Akinari; Fujii, Kentaro; Shikazono, Naoya; Ukai, Masatoshi*

Charged Particle and Photon Interactions with Matter; Recent Advances, Applications, and Interfaces, p.543 - 574, 2010/12

This review is one of the chapters of "Charged Particle and Photon Interactions with Matter; Recent Advances, Applications, and Interfaces". In this review we will introduce recent advances in spectroscopic study of DNA damage induced by ionizing radiation using synchrotron radiation and ion particles. Further, studies of susceptibility of DNA damage to enzymatic repair-processes revealed by biochemical techniques, as well as mutation assay for E. coli cells, will also be described and discussed by comparing with previous simulation data.

Synchrotron radiation photoelectron studies for primary radiation effects using a liquid water jet in vacuum; Total and partial photoelectron yields for liquid water mear the oxygen -edge

Ukai, Masatoshi*; Yokoya, Akinari; Nonaka, Yusuke*; Fujii, Kentaro; Saito, Yuji

Radiation Physics and Chemistry, 78(12), p.1202 - 1206, 2009/12

https://doi.org/10.1016/j.radphyschem.2009.07.011

To substantiate the hydrated structure of DNA from the view point of the electronic properties, we developed a new spectroscopic technique of photoelectrons ejected from solutions dissolving biological molecules using soft X-ray synchrotron radiation in combination with liquid jet in vacuum. The experiments are carried out at the BL23SU in SPring-8, Japan. The liquid sample is maintained in the form of continuous micro-beam ( = 20 m) in vacuum and is intersected by a well focused nearly micro-beam of synchrotron-radiation of less than 50 m. In this paper, we present (1) the partial yields of photoelectrons for liquid water molecules and oxygen Auger electron spectra in the energy range around the oxygen K-edge, and (2) the total photoelectron yields for DNA nucleotides (AMP, CMP, and GMP) in water solutions near nitrogen K-edge, which correspond to the X-ray absorption spectra (XANES).

X-ray absorption spectrum for guanosine-5'-monophosphate in water solution in the vicinity of the nitrogen K-edge observed in free liquid jet in vacuum

Ukai, Masatoshi*; Yokoya, Akinari; Fujii, Kentaro; Saito, Yuji

Radiation Physics and Chemistry, 77(10-12), p.1265 - 1269, 2008/10

https://doi.org/10.1016/j.radphyschem.2008.05.051

In order to substantiate the hydrated structure of DNA from the view point of the electronic properties, we develop a new spectroscopic technique for the photoelectrons ejected from solutions dissolving biological molecules using a soft X-ray synchrotron radiation (SPring-8, BL23SU) in combination with liquid jet technique in vacuum. In this paper, we present the first evidence of the spectrum of total photoelectron yields for a nucleotide, guanosine-5'-monophosphate, in solution in the energy region of so-called water window around nitrogen K-edge. A liquid nucleotide/water sample is maintained in the form of continuous thin water jet (diameter 20 m) in vacuum and is intersected by a highly focused soft X-ray beam. The obtained spectrum in solution shows common features with the spectrum in solid film. Nitrogen atoms only exist in the base site, so that the spectral similarities can be explained by the hydrophobic property of the base site.

Short-lived radicals induced in DNA-bases by oxygen and nitrogen K-shell photoexciation

Yokoya, Akinari; Fujii, Kentaro; Akamatsu, Ken; Ukai, Masatoshi*

no journal, , 

In order to obtain detailed insights into the physicochemical mechanism of DNA damage induction by oxygen and nitrogen K-shell photoexcitation, short-lived radicals induced in DNA-bases, adenine and guanine, were measured by applying an electroparamagnetic resonance (EPR) spectrometer at the SPring-8 soft X-ray beamline, BL23SU. The samples were prepared as an evaporated thin film in a vacuum chamber. Experimental evidence of the effect of water vapor on the yields of the base radicals will be discussed.