Ultrafast Damage Following Radiation‐Induced Oxidation of Uracil in Aqueous Solution

López‐Tarifa, Pablo; Gaigeot, Marie‐Pierre; Vuilleumier, Rodolphe; Tavernelli, Ivano; Alcamı́, Manuel; Martı́n, Fernando; Penhoat, Marie‐Anne Hervé du; Politis, M. F.

doi:10.1002/ange.201208038

Cited by 8 publications

(8 citation statements)

References 35 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Production of excited species from a water molecule by charge transfer reaction with doubly charged UMP ion is supposed to give rise to a much more energetic luminescence. The proposed charge transferring reaction between doubly charged UMP ion and a water molecule producing singly charged excited parent ion of UMP, with transfer of a single positive charge (e.g., a proton) to the hydrating water, is supported by previous reports (Lopez-Tarifa et al 2013, Fujii et al 2018. We have thus tentatively concluded that the present luminescence of aqueous UMP is due to singly charged parent ion species of UMP produced by the emission of a proton from doubly charged ions following Auger ionization of a N 1 s electron in uracil moiety.…”

Section: Resultssupporting

confidence: 78%

X-ray induced luminescence spectroscopy for DNA damaging intermediates aided by a monochromatic synchrotron radiation

Terao

Kumagai

Suzuki

et al. 2021

International Journal of Radiation Biology

View full text Add to dashboard Cite

Purpose: To identify the bonding sites of initial radiation interaction with DNA and to trace the following chemical reaction sequences on the pathway of damage induction, we carry out a spectroscopy XIL (X-ray induced luminescence) using soft X-ray synchrotron radiation. This is a nondestructive analysis of the excited intermediate species produced in a molecular mechanism on the damage induction pathway. Materials and Methods: We introduce aqueous samples of UMP (uridine-5'-monophosphate) in the vacuum by the use of a liquid micro-jet technique. The luminescence in the region of UV-VIS (from visible to ultraviolet) radiation induced after the absorption of monochromatic soft X-ray by aqueous UMP is measured with sweeping the soft X-ray energy in the region of 370-560 eV. Results: The enhanced XIL intensities for aqueous UMP in the region of soft X-ray of 410-530 eV (in "water window" region) are obtained. The enhancement of XIL intensities in the UV-VIS region, relative to the water control, is explained by the excitation and ionization of a K-shell electron of nitrogen atoms in the uracil moiety. The enhanced XIL intensities do not match the structure of XANES (X-ray absorption near-edge structure) of the aqueous UMP. This suggests that the XIL intensities reflect the quantum yields of luminescence, or the quantum yields for conversion by UMP of an absorbed X-ray into UV-VIS radiation. In this paper, spectra of luminescence are shown to be resolved by combining low pass filters. The filtered luminescence spectra are obtained at the center of gravity (kc) of the band pass wavelength regions at kc ¼ 270nm, 295 nm, 340 nm, 385 nm, 450 nm, and 525 nm., which show a trend similar to the fluorescence of nucleobases induced by ultraviolet radiation. Conclusion:It is concluded that the origin of the observed XIL is the hydrated uracil moiety in aqueous UMP, decomposition of which is suppressed by the migration of excess charge and internal energy after the double ionization due to Auger decay.

show abstract

Section: Resultssupporting

confidence: 78%

X-ray induced luminescence spectroscopy for DNA damaging intermediates aided by a monochromatic synchrotron radiation

Terao

Kumagai

Suzuki

et al. 2021

International Journal of Radiation Biology

View full text Add to dashboard Cite

show abstract

“…The RT-TDDFT approach is mostly used in the context of linear and nonlinear spectroscopies, 7,44,51−54 yet its scope was extended toward computational photodynamics. 14 It was used in order to investigate dynamics following Auger decay in water or nucleic acid bases, 55,56 to model low energy collisions between atoms and molecules, 57 radiation damage in materials, 58 or stopping power in the context of hadron therapies, 59−61 and for observing charge migration in molecules and dye-sensitized materials. 62,63 RT-TDDFT is on the other hand no panacea, and there are several issues to be addressed.…”

Section: ■ Introductionmentioning

confidence: 99%

Assessment of Real-Time Time-Dependent Density Functional Theory (RT-TDDFT) in Radiation Chemistry: Ionized Water Dimer

2018

View full text Add to dashboard Cite

Ionization in the condensed phase and molecular clusters leads to a complicated chain of processes with coupled electron-nuclear dynamics. It is difficult to describe such dynamics with conventional nonadiabatic molecular dynamics schemes since the number of states swiftly increases as the molecular system grows. It is therefore attractive to use a direct electron and nuclear propagation such as the real-time time-dependent density functional theory (RT-TDDFT). Here we report a RT-TDDFT benchmark study on simulations of singly and doubly ionized states of a water monomer and dimer as a prototype for more complex processes in a condensed phase. We employed the RT-TDDFT based Ehrenfest molecular dynamics with a generalized gradient approximate (GGA) functional and compared it with wave-function-based surface hopping (SH) simulations. We found that the initial dynamics of a singly HOMO ionized water dimer is similar for both the RT-TDDFT/GGA and the SH simulations but leads to completely different reaction channels on a longer time scale. This failure is attributed to the self-interaction error in the GGA functionals and it can be avoided by using hybrid functionals with large fraction of exact exchange (represented here by the BHandHLYP functional). The simulations of doubly ionized states are reasonably described already at the GGA level. This suggests that the RT-TDDFT/GGA method could describe processes following the autoionization processes such as Auger emission, while its applicability to more complex processes such as intermolecular Coulombic decay remains limited.

show abstract

“…To further investigate the early chemical reactions of the fragments within the sample, we switched to ground-state CP MD with a time step of 0.006 fs for a total simulation length of 1.3 ps. 15 When switching from TDDFT to CP MD, the positions and the velocities of all the atoms are kept unchanged, while the electronic structure is optimized to reach the BO surface, leading to a slight redistribution of the electronic cloud.…”

Section: ■ Computational Methodsmentioning

confidence: 99%

“…Indeed, the multitude of doubly ionized states are expected to be close in energy leading to fast nonadiabatic switches, which can quickly drive the system to the ground state. The dissociation of doubly ionized water 11 and uracil 15 molecules solution as well as isolated uracil 16 has already been reported.…”

Section: ■ Introductionmentioning

confidence: 91%

Proton Collision on Deoxyribose Originating from Doubly Ionized Water Molecule Dissociation

et al. 2018

Self Cite

View full text Add to dashboard Cite

In this work, we studied the fragmentation dynamics of 2-deoxy-d-ribose (DR) in solution that arises from the double ionization of a water molecule in its primary hydration shell. This process was modeled in the framework of ab initio molecular dynamics. The charge unbalanced in the solvent molecules produces a Coulomb explosion with the consequent release of protons with kinetic energy in the few electronvolts range, which collide with the surrounding molecules in solution inducing further chemical reactions. In particular, we observe proton collisions with the solute molecule DR, which leads to a complete ring opening. In DNA, damage to the DR moiety may lead to DNA strand breaking. This mechanism can be understood as one of the possible steps in the radiation-induced fragmentation of DNA chains.

show abstract

Ultrafast Damage Following Radiation‐Induced Oxidation of Uracil in Aqueous Solution

Cited by 8 publications

References 35 publications

X-ray induced luminescence spectroscopy for DNA damaging intermediates aided by a monochromatic synchrotron radiation

X-ray induced luminescence spectroscopy for DNA damaging intermediates aided by a monochromatic synchrotron radiation

Assessment of Real-Time Time-Dependent Density Functional Theory (RT-TDDFT) in Radiation Chemistry: Ionized Water Dimer

Proton Collision on Deoxyribose Originating from Doubly Ionized Water Molecule Dissociation

Contact Info

Product

Resources

About