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Nature Communications Nov 2023Time-resolved identification of surface-bound intermediates on metallic nanocatalysts is imperative to develop an accurate understanding of the elementary steps of CO...
Time-resolved identification of surface-bound intermediates on metallic nanocatalysts is imperative to develop an accurate understanding of the elementary steps of CO reduction. Direct observation on initial electron transfer to CO to form surface-bound CO radicals is lacking due to the technical challenges. Here, we use picosecond pulse radiolysis to generate CO via aqueous electron attachment and observe the stabilization processes toward well-defined nanoscale metallic sites. The time-resolved method combined with molecular simulations identifies surface-bound intermediates with characteristic transient absorption bands and distinct kinetics from nanosecond to the second timescale for three typical metallic nanocatalysts: Cu, Au, and Ni. The interfacial interactions are further investigated by varying the important factors, such as catalyst size and the presence of cation in the electrolyte. This work highlights fundamental ultrafast spectroscopy to clarify the critical initial step in the CO catalytic reduction mechanism.
PubMed: 37932333
DOI: 10.1038/s41467-023-42936-6 -
International Journal of Molecular... Jun 2021In this work, we use the next sub-volume method (NSM) to investigate the possibility of using the compartment-based ("on-lattice") model to simulate water radiolysis....
In this work, we use the next sub-volume method (NSM) to investigate the possibility of using the compartment-based ("on-lattice") model to simulate water radiolysis. We, first, start with a brief description of the reaction-diffusion master equation (RDME) in a spatially discretized simulation volume ("mesh"), which is divided into sub-volumes (or "voxels"). We then discuss the choice of voxel size and merging technique of a given mesh, along with the evolution of the system using the hierarchical algorithm for the RDME ("hRDME"). Since the compartment-based model cannot describe high concentration species of early radiation-induced spurs, we propose a combination of the particle-based step-by-step ("SBS") Brownian dynamics model and the compartment-based model ("SBS-RDME model") for the simulation. We, finally, use the particle-based SBS Brownian dynamics model of Geant4-DNA as a reference to test the model implementation through several benchmarks. We find that the compartment-based model can efficiently simulate the system with a large number of species and for longer timescales, beyond the microsecond, with a reasonable computing time. Our aim in developing this model is to study the production and evolution of reactive oxygen species generated under irradiation with different dose rate conditions, such as in FLASH and conventional radiotherapy.
Topics: Algorithms; Computer Simulation; DNA; Diffusion; Linear Energy Transfer; Models, Chemical; Models, Molecular; Monte Carlo Method; Pulse Radiolysis; Water
PubMed: 34199598
DOI: 10.3390/ijms22116023 -
Biomolecules Oct 2023We examined the reaction of hydroxyl radicals (HO) and sulfate radical anions (SO), which is generated by ionizing radiation in aqueous solutions under anoxic...
We examined the reaction of hydroxyl radicals (HO) and sulfate radical anions (SO), which is generated by ionizing radiation in aqueous solutions under anoxic conditions, with an alternating GC doubled-stranded oligodeoxynucleotide (ds-ODN), i.e., the palindromic 5'-d(GCGCGC)-3'. In particular, the optical spectra of the intermediate species and associated kinetic data in the range of ns to ms were obtained via pulse radiolysis. Computational studies by means of density functional theory (DFT) for structural and time-dependent DFT for spectroscopic features were performed on 5'-d(GCGC)-3'. Comprehensively, our results suggest the addition of HO to the G:C pair moiety, affording the [8-HO-G:C] detectable adduct. The previous reported spectra of one-electron oxidation of a variety of ds-ODN were assigned to [G(-H):C] after deprotonation. Regarding 5'-d(GCGCGC)-3' ds-ODN, the spectrum at 800 ns has a completely different spectral shape and kinetic behavior. By means of calculations, we assigned the species to [G:C/C:G], in which the electron hole is predicted to be delocalized on the two stacked base pairs. This transient species was further hydrated to afford the [8-HO-G:C] detectable adduct. These remarkable findings suggest that the double-stranded alternating GC sequences allow for a new type of electron hole stabilization via delocalization over the whole sequence or part of it.
Topics: Oligonucleotides; Hydroxyl Radical; Electrons; Free Radicals; Oxidation-Reduction; Oligodeoxyribonucleotides
PubMed: 37892175
DOI: 10.3390/biom13101493 -
Physical Chemistry Chemical Physics :... Sep 2021The early mechanisms by which ionizing rays damage biological structures by so-called direct effects are largely elusive. In a recent picosecond pulse radiolysis study...
The early mechanisms by which ionizing rays damage biological structures by so-called direct effects are largely elusive. In a recent picosecond pulse radiolysis study of concentrated uridine monophosphate solutions [J. Ma, S. A. Denisov, J.-L. Marignier, P. Pernot, A. Adhikary, S. Seki and M. Mostafavi, , 2018, , 5105], unexpected results were found regarding the oxidation of the nucleobase. The signature of the oxidized nucleobase could not be detected 5 ps after the electron pulse, but only the oxidized phosphate, raising intriguing questions about the identity of charge-transfer mechanisms that could explain the absence of U. We address here this question by means of advanced first-principles atomistic simulations of solvated uridine monophosphate, combining Density Functional Theory (DFT) with polarizable embedding schemes. We contrast three very distinct mechanisms of charge transfer covering the atto-, femto- and pico-second timescales. We first investigate the ionization mechanism and subsequent hole/charge migrations on a timescale of attoseconds to a few femtoseconds under the frozen nuclei approximation. We then consider a nuclear-driven phosphate-to-oxidized-nucleobase electron transfer, showing that it is an uncompetitive reaction channel on the sub-picosecond timescale, despite its high exothermicity and significant electronic coupling. Finally, we show that non-adiabatic charge transfer is enabled by femtosecond nuclear relaxation after ionization. We show that electronic decoherence and the electronic coupling strength are the key parameters that determine the hopping probabilities. Our results provide important insight into the interplay between electronics and nuclear motions in the early stages of the multiscale responses of biological matter subjected to ionizing radiation.
Topics: Density Functional Theory; Electron Transport; Helium; Ions; Molecular Dynamics Simulation; Uridine Monophosphate; Water
PubMed: 34528029
DOI: 10.1039/d0cp06482c -
Molecules (Basel, Switzerland) Aug 2019Thione-containing nucleobases have attracted the attention of the scientific community for their application in oncology, virology, and transplantology. The detailed...
Thione-containing nucleobases have attracted the attention of the scientific community for their application in oncology, virology, and transplantology. The detailed understanding of the reactivity of the purine derivative 8-thioguanosine (8-TG) with reactive oxygen species (ROS) and free radicals is crucial for its biological relevance. An extensive investigation on the fate of 8-TG under both reductive and oxidative conditions is here reported, and it was tested by employing steady-state photooxidation, laser flash photolysis, as well as γ-radiolysis in aqueous solutions. The characterization of the 8-TG T excited state by laser flash photolysis and the photooxidation experiments confirmed that singlet oxygen is a crucial intermediate in the formation of the unexpected reduced product guanosine, without the formation of the usual oxygenated sulfinic or sulfonic acids. Furthermore, a thorough screening of different radiolytic conditions upon γ-radiation afforded the reduced product. These results were rationalized by performing control experiments in the predominant presence of each reactive species formed by radiolysis of water, and the mechanistic pathway scenario was postulated on these bases.
Topics: Guanosine; Kinetics; Lasers; Light; Oxidation-Reduction; Photolysis; Pulse Radiolysis; Singlet Oxygen; Solutions; Thionucleosides; Water
PubMed: 31470553
DOI: 10.3390/molecules24173143 -
Journal of Inorganic Biochemistry Jan 2023Nitric oxide synthase (NOS) is a cytochrome P450-type mono‑oxygenase that catalyzes the oxidation of L-arginine to nitric oxide. We previously observed that...
Intramolecular electron transfer from biopterin to Fe-O complex in nitric oxide synthases occurs at very different rates between bacterial and mammalian enzymes: Direct observation of a catalytically active intermediate.
Nitric oxide synthase (NOS) is a cytochrome P450-type mono‑oxygenase that catalyzes the oxidation of L-arginine to nitric oxide. We previously observed that intramolecular electron transfer from biopterin to Fe-O in Deinococcus radiodurans NOS (DrNOS) using pulse radiolysis. However, the rate of electron transfer in DrNOS (2.2 × 10 s) contrasts with a reported corresponding rate (11 s) in a mammalian NOS determined using rapid freeze-quench (RFQ) EPR. We applied pulse radiolysis to Bacillus subtilis NOS (bsNOS) and to rat neural NOS oxygenase domain NOS (mNOS). Concurrently, RFQ EPR was used to trap a pterin radical during single-turnover enzyme reactions of the enzymes. By using the pulse radiolysis method, hydrated electrons (e) reduced the heme iron of NOS enzymes. Subsequently, ferrous heme reacted with O to form a Fe-O intermediate. In the presence of pterin, the intermediate of bsNOS was found to convert to other intermediate in the time range of milliseconds. A similar process was determined to have occurred after pulse radiolysis of the pterin-bound mNOS, though the rate was much slower. The intermediates of all of the NOS enzymes further converted to the original ferric form in the time range of seconds. When using the RFQ method, pterin radicals were formed very rapidly in both DrNOS and bsNOS in the time range of milliseconds. In contrast, the pterin radical in mNOS was observed to form slowly, at a rate of ∼20 s.
Topics: Animals; Rats; Arginine; Biopterins; Electrons; Ferrous Compounds; Heme; Iron; Nitric Oxide; Nitric Oxide Synthase; Oxidation-Reduction; Pterins; Bacillus subtilis
PubMed: 36327499
DOI: 10.1016/j.jinorgbio.2022.112035 -
Environmental Science & Technology May 2024Photoexcitation of sulfite (SO) is often used to generate hydrated electrons (e) in processes to degrade perfluoroalkyl and polyfluoroalkyl substances (PFASs)....
Photoexcitation of sulfite (SO) is often used to generate hydrated electrons (e) in processes to degrade perfluoroalkyl and polyfluoroalkyl substances (PFASs). Conventional consensus discourages the utilization of SO concentrations exceeding 10 mM for effective defluorination. This has hindered our understanding of SO chemistry beyond its electron photogeneration properties. In contrast, the radiation-chemical study presented here, directly producing e through water radiolysis, suggests that SO plays a previously overlooked activation role in the defluorination. Quantitative Co gamma irradiation experiments indicate that the increased SO concentration from 0.1 to 1 M enhances the defluorination rate by a remarkable 15-fold, especially for short-chain perfluoroalkyl sulfonate (PFSA). Furthermore, during the treatment of long-chain PFSA (CF-SO) with a higher concentration of SO, the intermediates of CH-SO and CF-COO were observed, which are absent without SO. These observations highlight that a higher concentration of SO facilitates both reaction pathways: chain shortening and H/F exchange. Pulse radiolysis measurements show that elevated SO concentrations accelerate the bimolecular reaction between e and PFSA by 2 orders of magnitude. F NMR measurements and theoretical simulations reveal the noncovalent interactions between SO and F atoms, which exceptionally reduce the C-F bond dissociation energy by nearly 40%. As a result, our study offers a more effective strategy for degrading highly persistent PFSA contaminants.
Topics: Sulfites; Electrons; Fluorocarbons; Water
PubMed: 38747404
DOI: 10.1021/acs.est.4c01444 -
The Journal of Physical Chemistry. A Jan 2023Transient chemistry of sensitizing dyes is important to obtain insights into the photochemical conversion processes of light harvesting assemblies. We have now employed...
Transient chemistry of sensitizing dyes is important to obtain insights into the photochemical conversion processes of light harvesting assemblies. We have now employed transient absorption spectroscopy (pulsed laser and pulse radiolysis) to characterize the excited state and radical intermediates of a perylene derivative, (5,10,15,20-Tetraphenylbisbenz[5,6]indeno[1,2,3-:1',2',3'-]perylene (DBP). The distinguishable transient absorption features for the singlet and triplet excited states and radical anion and radical cation provide spectral fingerprints to identify the reaction intermediates in photochemical energy and electron transfer processes of composite systems involving DBP. For example, identifying these transients in the energy transfer processes of the rubrene-DBP system would aid in establishing their role as annihilator-emitter for triplet-triplet annihilation up-conversion (TTA-UC). The transient characterization thus serves as an important mechanistic fingerprint for elucidating mechanistic details of systems employing DBP in optoelectronic applications.
PubMed: 36375093
DOI: 10.1021/acs.jpca.2c06904 -
Chemosphere May 2024The paper presents the results of studying the efficiency of the bisphenol A transformation in water exposed to ultraviolet radiation and a high-energy-pulse-electron...
The paper presents the results of studying the efficiency of the bisphenol A transformation in water exposed to ultraviolet radiation and a high-energy-pulse-electron beam (e-beam). It has been shown that in both cases, degradation of dissolved bisphenol A occurs, accompanied by an increase in the absorption coefficient in the wavelength region of more than 300 nm. After exposure, products were recorded that fluoresced in the region of more than λ = 400 nm. The fluorescent transformation product of bisphenol A in water (λ = 425 nm) was maximum formatted after an KrCl excilamp irradiated, and under the action of an e-beam, the accumulation of this product was minimal. Under e-beam radiation (170 keV) the efficiency of bisphenol A (1 mM) removal reached 97%. The data obtained allow us to develop ideas about photolysis and radiolysis in natural water systems when knowledge about targeted and optimal conditions for the degradation of bisphenol A is needed.
Topics: Benzhydryl Compounds; Phenols; Ultraviolet Rays; Photolysis; Water Pollutants, Chemical; Electrons; Water Purification
PubMed: 38556183
DOI: 10.1016/j.chemosphere.2024.141802 -
Chemphyschem : a European Journal of... Mar 2023Acetohydroxamic acid (AHA) has been proposed for inclusion in advanced, single-cycle, used nuclear fuel reprocessing solvent systems for the reduction and complexation...
Acetohydroxamic acid (AHA) has been proposed for inclusion in advanced, single-cycle, used nuclear fuel reprocessing solvent systems for the reduction and complexation of plutonium and neptunium ions. For this application, a detailed description of the fundamental degradation of AHA in dilute aqueous nitric acid is required. To this end, we present a comprehensive, multiscale computer model for the coupled radiolytic and hydrolytic degradation of AHA in aqueous sodium nitrate and nitric acid solutions. Rate coefficients for the reactions of AHA and hydroxylamine (HA) with the oxidizing nitrate radical were measured for the first time using electron pulse radiolysis and used as inputs for the kinetic model. The computer model results are validated by comparison to experimental data from steady-state gamma ray irradiations, for which the agreement is excellent. The presented model accurately predicts the yields of the major degradation products of AHA: acetic acid, HA, nitrous oxide, and molecular hydrogen.
PubMed: 36470592
DOI: 10.1002/cphc.202200749