1
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Alikhani ME, Madebène B, Silvi B. Microsolvation of cobalt, nickel, and copper atoms with ammonia: a theoretical study of the solvated electron precursors. J Mol Model 2024; 30:220. [PMID: 38902588 DOI: 10.1007/s00894-024-06019-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 06/10/2024] [Indexed: 06/22/2024]
Abstract
CONTEXT The s-block metals dissolved in ammonia form metal-ammonia complexes with diffuse electrons which could be used for redox catalysis. In this theoretical paper, we investigated the possibility of the d-bloc transition metals (Mn, Fe, Co, Ni, and Cu) solvated by ammonia. It has been demonstrated that both Mn and Fe atoms undergo into an oxidative reaction with NH3 forming an inserted species, HMNH2. On the contrary, the Co, Ni, and Cu atoms can accommodate four NH3, via the coordination bond, to form the first solvation sphere within C2v, D2d, and Td point groups, respectively. Addition of a fifth NH3 constitute the second solvation shell by forming hydrogen bond with the other NH3s. Interestingly, M(NH3)4 (M = Co, Ni, and Cu) is a so-called solvated electron precursor and should be considered as a monocation M(NH3)4+ kernel in tight contact with one electron distributed over its periphery. This nearly free electron could be used to capture a CO2 molecule and engages in a reduction reaction. METHODS Geometry optimization of the stationary points on the potential energy surface was performed using density functional theory - CAM-B3LYP functional including the GD3BJ dispersion contribution - in combination with the 6-311 + + G(2d, 2p) basis set for all the atoms. All first-principles calculations were performed using the Gaussian 09 quantum chemical packages. The natural electron configuration of transition atom engaged in the compounds has been found using the natural bond orbital (NBO) method. We used the EDR (electron delocalization range) approach to analyze the structure of solvated electrons in real space. We also used the electron localization function (ELF) to measure the degree of electronic localization within a chemical compound. The EDR and ELF analyses are done using the TopMod and Multiwfn packages, respectively.
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Affiliation(s)
| | - Bruno Madebène
- Sorbonne Université CNRS, MONARIS, UMR8233, F-75005, Paris, France
| | - Bernard Silvi
- Sorbonne Université CNRS, LCT, UMR7616, F-75005, Paris, France
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2
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Chen M, Moher D, Rogers J, Yatom S, Thimsen E, Parker KM. Effects of Halides on Organic Compound Degradation during Plasma Treatment of Brines. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:5139-5152. [PMID: 38446791 DOI: 10.1021/acs.est.3c07162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/08/2024]
Abstract
Plasma has been proposed as an alternative strategy to treat organic contaminants in brines. Chemical degradation in these systems is expected to be partially driven by halogen oxidants, which have been detected in halide-containing solutions exposed to plasma. In this study, we characterized specific mechanisms involving the formation and reactions of halogen oxidants during plasma treatment. We first demonstrated that addition of halides accelerated the degradation of a probe compound known to react quickly with halogen oxidants (i.e., para-hydroxybenzoate) but did not affect the degradation of a less reactive probe compound (i.e., benzoate). This effect was attributed to the degradation of para-hydroxybenzoate by hypohalous acids, which were produced via a mechanism involving halogen radicals as intermediates. We applied this mechanistic insight to investigate the impact of constituents in brines on reactions driven by halogen oxidants during plasma treatment. Bromide, which is expected to occur alongside chloride in brines, was required to enable halogen oxidant formation, consistent with the generation of halogen radicals from the oxidation of halides by hydroxyl radical. Other constituents typically present in brines (i.e., carbonates, organic matter) slowed the degradation of organic compounds, consistent with their ability to scavenge species involved during plasma treatment.
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Affiliation(s)
- Moshan Chen
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Dillon Moher
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Jacqueline Rogers
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Shurik Yatom
- Princeton Plasma Physics Laboratory, Princeton University, Princeton, New Jersey 08540 , United States
| | - Elijah Thimsen
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Kimberly M Parker
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
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3
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Jaiswal VK, Kabaciński P, Nogueira de Faria BE, Gentile M, de Paula AM, Borrego-Varillas R, Nenov A, Conti I, Cerullo G, Garavelli M. Environment-Driven Coherent Population Transfer Governs the Ultrafast Photophysics of Tryptophan. J Am Chem Soc 2022; 144:12884-12892. [PMID: 35796759 PMCID: PMC9305959 DOI: 10.1021/jacs.2c04565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
By combining UV transient
absorption spectroscopy with sub-30-fs
temporal resolution and CASPT2/MM calculations, we present a complete
description of the primary photoinduced processes in solvated tryptophan.
Our results shed new light on the role of the solvent in the relaxation
dynamics of tryptophan. We unveil two consecutive coherent population
transfer events involving the lowest two singlet excited states: a
sub-50-fs nonadiabatic La → Lb transfer
through a conical intersection and a subsequent 220 fs reverse Lb → La transfer due to solvent-assisted adiabatic
stabilization of the La state. Vibrational fingerprints
in the transient absorption spectra provide compelling evidence of
a vibronic coherence established between the two excited states from
the earliest times after photoexcitation and lasting until the back-transfer
to La is complete. The demonstration of response to the
environment as a driver of coherent population dynamics among the
excited states of tryptophan closes the long debate on its solvent-assisted
relaxation mechanisms and extends its application as a local probe
of protein dynamics to the ultrafast time scales.
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Affiliation(s)
- Vishal Kumar Jaiswal
- Dipartimento di Chimica industriale "Toso Montanari", Università di Bologna, Viale del Risorgimento 4, 40136 Bologna, Italy
| | - Piotr Kabaciński
- Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milano, Italy
| | | | - Marziogiuseppe Gentile
- Dipartimento di Chimica industriale "Toso Montanari", Università di Bologna, Viale del Risorgimento 4, 40136 Bologna, Italy
| | - Ana Maria de Paula
- Departamento de Física, Universidade Federal de Minas Gerais, 31270-901 Belo Horizonte-MG, Brazil
| | - Rocio Borrego-Varillas
- Istituto di Fotonica e Nanotecnologie, CNR-IFN, Piazza Leonardo da Vinci 32, 20133 Milano, Italy
| | - Artur Nenov
- Dipartimento di Chimica industriale "Toso Montanari", Università di Bologna, Viale del Risorgimento 4, 40136 Bologna, Italy
| | - Irene Conti
- Dipartimento di Chimica industriale "Toso Montanari", Università di Bologna, Viale del Risorgimento 4, 40136 Bologna, Italy
| | - Giulio Cerullo
- Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milano, Italy.,Istituto di Fotonica e Nanotecnologie, CNR-IFN, Piazza Leonardo da Vinci 32, 20133 Milano, Italy
| | - Marco Garavelli
- Dipartimento di Chimica industriale "Toso Montanari", Università di Bologna, Viale del Risorgimento 4, 40136 Bologna, Italy
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4
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Pios S, Domcke W. Ab Initio Electronic Structure Study of the Photoinduced Reduction of Carbon Dioxide with the Heptazinyl Radical. J Phys Chem A 2022; 126:2778-2787. [PMID: 35476421 DOI: 10.1021/acs.jpca.2c00615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The photocatalytic conversion of carbon dioxide to liquid fuels with electrons taken from water with solar photons is one of the grand goals of renewable energy research. Polymeric carbon nitrides recently emerged as metal-free materials with promising functionalities for hydrogen evolution from water as well as the activation of carbon dioxide. Molecular heptazine (Hz), the building block of polymeric carbon nitrides, is one the strongest known organic photo-oxidants and has been shown to be able to photo-oxidize water with near-visible light, resulting in reduced (hydrogenated) heptazine (HzH) and OH radicals. In the present work, we explored with ab initio computational methods whether the HzH chromophore is able to reduce carbon dioxide to the hydroxy-formyl (HOCO) radical in hydrogen-bonded HzH-CO2 complexes by the absorption of a photon. In remarkable contrast to the high barrier for carbon dioxide activation in the electronic ground state, the excited-state proton-coupled electron transfer (PCET) reaction is nearly barrierless, but requires the diabatic passage of three conical intersections. The possibility of barrierless carbon dioxide activation by excited-state PCET has so far not been taken into consideration in the interpretation of photocatalytic carbon dioxide reduction on carbon nitride materials.
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Affiliation(s)
- Sebastian Pios
- Department of Chemistry, Technical University of Munich, D-85747 Garching, Germany
| | - Wolfgang Domcke
- Department of Chemistry, Technical University of Munich, D-85747 Garching, Germany
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5
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Mi D, Xu J, Zhang Y, Zhu T, Ouyang J, Dong X, Chingin K. Formation of protonated water-hydrogen clusters in an ion trap mass spectrometer at room temperature. Phys Chem Chem Phys 2022; 24:7180-7184. [PMID: 35128554 DOI: 10.1039/d1cp04516d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Protonated water-hydrogen clusters [H+(H2O)n·m(H2)] present an interesting model for fundamental water research, but their formation and isolation presents considerable experimental challenges. Here, we report the detection of [H+(H2O)n·m(H2)] (2 ≤ n ≤ 3, m ≤ 2) clusters alongside protonated water clusters H+(H2O)n (2 ≤ n ≤ 3) in a linear ion trap mass spectrometer under two different experimental conditions: (1) when water vapor was ionized by +5.5 kV ambient corona discharge in front of the mass spectrometer inlet; (2) when isolated H+(H2O)n clusters were exposed to H2 gas inside the linear trap. Chemical assignment of [H+(H2O)n·m(H2)] clusters was confirmed using reference experiments with isotopically labeled water and deuterium. Also, the formation of H2 gas in the corona discharge area was indicated by a flame test. Overall, our findings clearly indicate that [H+(H2O)n·m(H2)] clusters can be produced at room temperature through the association of protonated water clusters H+(H2O)n with H2 gas, without any cooling necessary. A mechanism for the formation of the protonated water-hydrogen complexes was proposed. Our results also suggest that the association of water ions with H2 gas may play a notable role in corona discharge ionization processes, such as atmospheric pressure chemical ionization, and may be partially responsible for the stabilization of reactive radical species occasionally reported in corona discharge ionization experiments.
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Affiliation(s)
- Dongbo Mi
- Jiangxi Key Laboratory for Mass Spectrometry and Instrumentation, East China University of Technology, Nanchang 330013, China.
| | - Junqiang Xu
- Jiangxi Key Laboratory for Mass Spectrometry and Instrumentation, East China University of Technology, Nanchang 330013, China.
| | - Yunpeng Zhang
- Jiangxi Key Laboratory for Mass Spectrometry and Instrumentation, East China University of Technology, Nanchang 330013, China.
| | - Tenggao Zhu
- Jiangxi Key Laboratory for Mass Spectrometry and Instrumentation, East China University of Technology, Nanchang 330013, China.
| | - Jiewen Ouyang
- Jiangxi Key Laboratory for Mass Spectrometry and Instrumentation, East China University of Technology, Nanchang 330013, China.
| | - Xiaofeng Dong
- Jiangxi Key Laboratory for Mass Spectrometry and Instrumentation, East China University of Technology, Nanchang 330013, China.
| | - Konstantin Chingin
- Jiangxi Key Laboratory for Mass Spectrometry and Instrumentation, East China University of Technology, Nanchang 330013, China.
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6
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Bachman B, Zhu D, Bandy J, Zhang L, Hamers RJ. Detection of Aqueous Solvated Electrons Produced by Photoemission from Solids Using Transient Absorption Measurements. ACS MEASUREMENT SCIENCE AU 2022; 2:46-56. [PMID: 36785590 PMCID: PMC9838729 DOI: 10.1021/acsmeasuresciau.1c00025] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Solvated electrons in water have long been of interest to chemists. While readily produced using intense multiphoton excitation of water and/or irradiation with high-energy particles, the possible role of solvated electrons in electrochemical and photoelectrochemical reactions at electrodes has been controversial. Recent studies showed that excitation of electrons to the conduction band of diamond leads to barrier-free emission of electrons into water. While these electrons can be inferred from the reactions they induce, direct detection by transient absorption measurements provides more direct evidence. Here, we present studies demonstrating direct detection of solvated electrons produced at diamond electrode surfaces and the influence of electrochemical potential and solution-phase electron scavengers. We further present a more detailed analysis of experimental conditions needed to detect solvated electrons emitted from diamond and other solid materials through transient optical absorption measurements.
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7
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Ahmadi S. Hydrated electrons and cluster science. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.131898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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8
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Patel J, Keshvani MJ. Study of Plasma–Water Interactions: Effect of Plasma Electrons and Production of Hydrogen Peroxide. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2021. [DOI: 10.1134/s0036024421130161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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9
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Seferji KA, Susapto HH, Khan BK, Rehman ZU, Abbas M, Emwas AH, Hauser CAE. Green Synthesis of Silver-Peptide Nanoparticles Generated by the Photoionization Process for Anti-Biofilm Application. ACS APPLIED BIO MATERIALS 2021; 4:8522-8535. [PMID: 35005954 DOI: 10.1021/acsabm.1c01013] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
An alarming increase in antibiotic-resistant bacterial strains is driving clinical demand for new antibacterial agents. One of the oldest antimicrobial agents is elementary silver (Ag), which has been used for thousands of years. Even today, elementary Ag is used for medical purposes such as treating burns, wounds, and microbial infections. In consideration of the effectiveness of elementary Ag, the present researchers generated effective antibacterial/antibiofilm agents by combining elementary Ag with biocompatible ultrashort peptide compounds. The innovative antibacterial agents comprised a hybrid peptide bound to Ag nanoparticles (IVFK/Ag NPs). These were generated by photoionizing a biocompatible ultrashort peptide, thus reducing Ag ions to form Ag NPs with a diameter of 6 nm. The IVFK/Ag NPs demonstrated promising antibacterial/antibiofilm activity against reference Gram-positive and Gram-negative bacteria compared with commercial Ag NPs. Through morphological changes in Escherichia coli and Staphylococcus aureus, we proposed that the mechanism of action for IVFK/Ag NPs derives from their ability to disrupt bacterial membranes. In terms of safety, the IVFK/Ag NPs demonstrated biocompatibility in the presence of human dermal fibroblast cells, and concentrations within the minimal inhibitory concentration had no significant effect on cell viability. These results demonstrated that hybrid peptide/Ag NPs hold promise as a biocompatible material with strong antibacterial/antibiofilm properties, allowing them to be applied across a wide range of applications in tissue engineering and regenerative medicine.
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Affiliation(s)
- Kholoud A Seferji
- Laboratory for Nanomedicine, Division of Biological & Environmental Science & Engineering (BESE), King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia.,Biology Department, Faculty of Science, Taibah University, Al-Madinah Al-Munawarah 41411, Saudi Arabia
| | - Hepi Hari Susapto
- Laboratory for Nanomedicine, Division of Biological & Environmental Science & Engineering (BESE), King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Babar K Khan
- Water Desalination and Reuse Center (WDRC), King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Zahid U Rehman
- Water Desalination and Reuse Center (WDRC), King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Manzar Abbas
- Laboratory for Nanomedicine, Division of Biological & Environmental Science & Engineering (BESE), King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Abdul-Hamid Emwas
- Core Labs, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Charlotte A E Hauser
- Laboratory for Nanomedicine, Division of Biological & Environmental Science & Engineering (BESE), King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia.,Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
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10
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Prasselsperger A, Coughlan M, Breslin N, Yeung M, Arthur C, Donnelly H, White S, Afshari M, Speicher M, Yang R, Villagomez-Bernabe B, Currell FJ, Schreiber J, Dromey B. Real-Time Electron Solvation Induced by Bursts of Laser-Accelerated Protons in Liquid Water. PHYSICAL REVIEW LETTERS 2021; 127:186001. [PMID: 34767414 DOI: 10.1103/physrevlett.127.186001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 09/24/2021] [Indexed: 06/13/2023]
Abstract
Understanding the mechanisms of proton energy deposition in matter and subsequent damage formation is fundamental to radiation science. Here we exploit the picosecond (10^{-12} s) resolution of laser-driven accelerators to track ultrafast solvation dynamics for electrons due to proton radiolysis in liquid water (H_{2}O). Comparing these results with modeling that assumes initial conditions similar to those found in photolysis reveals that solvation time due to protons is extended by >20 ps. Supported by magnetohydrodynamic theory this indicates a highly dynamic phase in the immediate aftermath of the proton interaction that is not accounted for in current models.
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Affiliation(s)
- A Prasselsperger
- Fakultät für Physik, Ludwig-Maximilians-Universität München, 85748 Garching, Germany
- Centre for Plasma Physics, School of Mathematics and Physics, Queens University Belfast, Belfast BT7 1NN, United Kingdom
| | - M Coughlan
- Centre for Plasma Physics, School of Mathematics and Physics, Queens University Belfast, Belfast BT7 1NN, United Kingdom
| | - N Breslin
- Centre for Plasma Physics, School of Mathematics and Physics, Queens University Belfast, Belfast BT7 1NN, United Kingdom
| | - M Yeung
- Centre for Plasma Physics, School of Mathematics and Physics, Queens University Belfast, Belfast BT7 1NN, United Kingdom
| | - C Arthur
- Centre for Plasma Physics, School of Mathematics and Physics, Queens University Belfast, Belfast BT7 1NN, United Kingdom
| | - H Donnelly
- Centre for Plasma Physics, School of Mathematics and Physics, Queens University Belfast, Belfast BT7 1NN, United Kingdom
| | - S White
- Centre for Plasma Physics, School of Mathematics and Physics, Queens University Belfast, Belfast BT7 1NN, United Kingdom
| | - M Afshari
- Centre for Plasma Physics, School of Mathematics and Physics, Queens University Belfast, Belfast BT7 1NN, United Kingdom
| | - M Speicher
- Fakultät für Physik, Ludwig-Maximilians-Universität München, 85748 Garching, Germany
| | - R Yang
- Fakultät für Physik, Ludwig-Maximilians-Universität München, 85748 Garching, Germany
| | - B Villagomez-Bernabe
- The Dalton Cumbria Facility and the School of Chemistry, The University of Manchester, Oxford Rd, Manchester M13 9PL, United Kingdom
| | - F J Currell
- The Dalton Cumbria Facility and the School of Chemistry, The University of Manchester, Oxford Rd, Manchester M13 9PL, United Kingdom
| | - J Schreiber
- Fakultät für Physik, Ludwig-Maximilians-Universität München, 85748 Garching, Germany
| | - B Dromey
- Centre for Plasma Physics, School of Mathematics and Physics, Queens University Belfast, Belfast BT7 1NN, United Kingdom
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11
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Iwe N, Raspe K, Müller M, Martinez F, Schweikhard L, Meiwes-Broer KH, Tiggesbäumker J. Size and charge-state dependence of detachment energies of polyanionic silver clusters. J Chem Phys 2021; 155:164303. [PMID: 34717355 DOI: 10.1063/5.0068278] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The electronic properties of silver clusters (N up to 800) charged by attachment of up to z = 7 excess electrons are investigated. As an essential preparation step, the technique of in-trap electron attachment to size-selected monoanions within a linear Paul trap is applied. By taking advantage of tunable laser pulses, the photoelectron spectra allow us to evaluate details of the electronic structure of polyanionic metal clusters, giving a multidimensional dataset. The subsequent analysis based on the liquid drop model provides information about the atomic structure and the bulk work function at a hitherto unknown quality.
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Affiliation(s)
- N Iwe
- Institute of Physics, University of Rostock, 18059 Rostock, Germany
| | - K Raspe
- Institute of Physics, University of Rostock, 18059 Rostock, Germany
| | - M Müller
- Institute of Physics, University of Rostock, 18059 Rostock, Germany
| | - F Martinez
- Institute of Physics, University of Rostock, 18059 Rostock, Germany
| | - L Schweikhard
- Institute of Physics, University of Greifswald, 17489 Greifswald, Germany
| | - K-H Meiwes-Broer
- Institute of Physics, University of Rostock, 18059 Rostock, Germany
| | - J Tiggesbäumker
- Institute of Physics, University of Rostock, 18059 Rostock, Germany
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12
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de Almeida JM, Nguyen NL, Colonna N, Chen W, Rodrigues Miranda C, Pasquarello A, Marzari N. Electronic Structure of Water from Koopmans-Compliant Functionals. J Chem Theory Comput 2021; 17:3923-3930. [PMID: 34137253 DOI: 10.1021/acs.jctc.1c00063] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Obtaining a precise theoretical description of the spectral properties of liquid water poses challenges for both molecular dynamics (MD) and electronic structure methods. The lower computational cost of the Koopmans-compliant functionals with respect to Green's function methods allows the simulations of many MD trajectories, with a description close to the state-of-art quasi-particle self-consistent GW plus vertex corrections method (QSGW + fxc). Thus, we explore water spectral properties when different MD approaches are used, ranging from classical MD to first-principles MD, and including nuclear quantum effects. We have observed that different MD approaches lead to up to 1 eV change in the average band gap; thus, we focused on the band gap dependence with the geometrical properties of a system to explain such spread. We have evaluated the changes in the band gap due to variations in the intramolecular O-H bond distance and HOH angle, as well as the intermolecular hydrogen bond O···O distance and the OHO angles. We have observed that the dominant contribution comes from the O-H bond length; the O···O distance plays a secondary role, and the other geometrical properties do not significantly influence the gap. Furthermore, we analyze the electronic density of states (DOS), where the KIPZ functional shows good agreement with the DOS obtained with state-of-art approaches employing quasi-particle self-consistent GW plus vertex corrections. The O-H bond length also significantly influences the DOS. When nuclear quantum effects are considered, broadening of the peaks driven by the broader distribution of the O-H bond lengths is observed, leading to a closer agreement with the experimental photoemission spectra.
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Affiliation(s)
- James Moraes de Almeida
- Universidade Federal do ABC, Centro de Ciências Naturais e Humanas, Santo André, 09210-580 SP, Brazil.,Theory and Simulation of Materials (THEOS) and National Centre for Computational Design and Discovery of Novel Materials (MARVEL), Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Ngoc Linh Nguyen
- Theory and Simulation of Materials (THEOS) and National Centre for Computational Design and Discovery of Novel Materials (MARVEL), Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Nicola Colonna
- Laboratory for Neutron Scattering and Imaging, Paul Scherrer Institute, CH-5232 Villigen-PSI, Switzerland.,National Centre for Computational Design and Discovery of Novel Materials (MARVEL), École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Wei Chen
- Institute of Condensed Matter and Nanoscience, Université Catholique de Louvain, B-1348 Louvain-la-Neuve, Belgium
| | | | - Alfredo Pasquarello
- Chaire de Simulation à l'Echelle Atomique (CSEA), Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Nicola Marzari
- Theory and Simulation of Materials (THEOS) and National Centre for Computational Design and Discovery of Novel Materials (MARVEL), Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
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13
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Pshenichnyuk SA, Modelli A. Electron Attachment to Isolated Molecules as a Probe to Understand Mitochondrial Reductive Processes. Methods Mol Biol 2021; 2277:101-124. [PMID: 34080147 DOI: 10.1007/978-1-0716-1270-5_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
This chapter describes the complementary experimental techniques Electron Transmission Spectroscopy and Dissociative Electron Attachment Spectroscopy, two of the most suitable means for investigating interactions between electrons and gas-phase molecules, resonance formation of temporary molecular negative ions, and their possible decay through the dissociative electron attachment (DEA) mechanism. The latter can be seen as the gas-phase counterpart of the transfer of a solvated electron in solution, accompanied by dissociation of the molecular anion, referred to as dissociative electron transfer (DET). DET takes place in vivo under reductive conditions, for instance, in the intermembrane space of mitochondria under interaction of xenobiotic molecules possessing high electron affinity with electrons "leaked" from the mitochondrial respiratory chain. A likely mechanism of the toxic activity of dichlorodiphenyltrichloroethane based on its DEA properties is briefly outlined, and compared with the well-established harmful effects of the model toxicant carbon tetrachloride ascribed to reductive dechlorination in a cellular ambient. A possible mechanism of the antioxidant activity of polyphenolic compounds present near the main site of superoxide anion production in mitochondria is also briefly discussed.
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Affiliation(s)
- Stanislav A Pshenichnyuk
- Institute of Molecule and Crystal Physics, Ufa Federal Research Centre, Russian Academy of Sciences, Ufa, Russia.
| | - Alberto Modelli
- Dipartimento di Chimica "G. Ciamician", Università di Bologna, Bologna, Italy
- Centro Interdipartimentale di Ricerca in Scienze Ambientali, Ravenna, Italy
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14
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15
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Kitajima K, Nakai Y, Sameera WMC, Tsuge M, Miyazaki A, Hidaka H, Kouchi A, Watanabe N. Delivery of Electrons by Proton-Hole Transfer in Ice at 10 K: Role of Surface OH Radicals. J Phys Chem Lett 2021; 12:704-710. [PMID: 33400539 DOI: 10.1021/acs.jpclett.0c03345] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Although water ice has been widely accepted to carry a positive charge via the transfer of excess protons through a hydrogen-bonded system, ice was recently found to be a negative charge conductor upon simultaneous exposure to electrons and ultraviolet photons at temperatures below 50 K. In this work, the mechanism of electron delivery was confirmed experimentally by both measuring currents through ice and monitoring photodissociated OH radicals on ice by using a novel method. The surface OH radicals significantly decrease upon the appearance of negative current flow, indicating that the electrons are delivered by proton-hole (OH-) transfer in ice triggered by OH- production on the surface. The mechanism of proton-hole transfer was rationalized by density functional theory calculations.
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Affiliation(s)
- Kensei Kitajima
- Institute of Low Temperature Science, Hokkaido University, Sapporo 060-0819, Japan
| | - Yoichi Nakai
- Radioactive Isotope Physics Laboratory, RIKEN Nishina Center, Saitama 351-0198, Japan
| | - W M C Sameera
- Institute of Low Temperature Science, Hokkaido University, Sapporo 060-0819, Japan
| | - Masashi Tsuge
- Institute of Low Temperature Science, Hokkaido University, Sapporo 060-0819, Japan
| | - Ayane Miyazaki
- Institute of Low Temperature Science, Hokkaido University, Sapporo 060-0819, Japan
| | - Hiroshi Hidaka
- Institute of Low Temperature Science, Hokkaido University, Sapporo 060-0819, Japan
| | - Akira Kouchi
- Institute of Low Temperature Science, Hokkaido University, Sapporo 060-0819, Japan
| | - Naoki Watanabe
- Institute of Low Temperature Science, Hokkaido University, Sapporo 060-0819, Japan
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16
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Lapointe F, Wolf M, Campen RK, Tong Y. Probing the Birth and Ultrafast Dynamics of Hydrated Electrons at the Gold/Liquid Water Interface via an Optoelectronic Approach. J Am Chem Soc 2020; 142:18619-18627. [PMID: 32954719 PMCID: PMC7596759 DOI: 10.1021/jacs.0c08289] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
The hydrated electron
has fundamental and practical significance
in radiation and radical chemistry, catalysis, and radiobiology. While
its bulk properties have been extensively studied, its behavior at
solid/liquid interfaces is still unclear due to the lack of effective
tools to characterize this short-lived species in between two condensed
matter layers. In this study, we develop a novel optoelectronic technique
for the characterization of the birth and structural evolution of
solvated electrons at the metal/liquid interface with a femtosecond
time resolution. Using this tool, we record for the first time the
transient spectra (in a photon energy range from 0.31 to 1.85 eV) in situ with a time resolution of 50 fs revealing several
novel aspects of their properties at the interface. Especially the
transient species show state-dependent optical transition behaviors
from being isotropic in the hot state to perpendicular to the surface
in the trapped and solvated states. The technique will enable a better
understanding of hot electron driven reactions at electrochemical
interfaces.
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Affiliation(s)
- François Lapointe
- Fritz Haber Institute of the Max Planck Society, Faradayweg 4-6, 14195 Berlin, Germany
| | - Martin Wolf
- Fritz Haber Institute of the Max Planck Society, Faradayweg 4-6, 14195 Berlin, Germany
| | - R Kramer Campen
- Fritz Haber Institute of the Max Planck Society, Faradayweg 4-6, 14195 Berlin, Germany.,Faculty of Physics, University of Duisburg-Essen, Lotharstrasse 1, 47057 Duisburg, Germany
| | - Yujin Tong
- Fritz Haber Institute of the Max Planck Society, Faradayweg 4-6, 14195 Berlin, Germany.,Faculty of Physics, University of Duisburg-Essen, Lotharstrasse 1, 47057 Duisburg, Germany
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17
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Hahn MB, Smales GJ, Seitz H, Solomun T, Sturm H. Ectoine interaction with DNA: influence on ultraviolet radiation damage. Phys Chem Chem Phys 2020; 22:6984-6992. [PMID: 32188961 DOI: 10.1039/d0cp00092b] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Ectoine is a small zwitterionic osmolyte and compatible solute, which does not interfere with cell metabolism even at molar concentrations. Plasmid DNA (pUC19) was irradiated with ultraviolet radiation (UV-C at 266 nm) under quasi physiological conditions (PBS) and in pure water in the presence and absence of ectoine (THP(B)) and hydroxyectoine (THP(A)). Different types of UV induced DNA damage were analysed: DNA single-strand breaks (SSBs), abasic sites and cyclobutane pyrimidine dimers (CPDs). A complex interplay between these factors was observed with respect to the nature and occurrence of DNA damage with 266 nm photons. In PBS, the cosolutes showed efficient protection against base damage, whilst in pure water, a dramatic shift from SSB damage to base damage was observed when cosolutes were added. To test whether these effects are caused by ectoine binding to DNA, further experiments were conducted: small-angle X-ray scattering (SAXS), surface-plasmon resonance (SPR) measurements and Raman spectroscopy. The results show, for the first time, a close interaction between ectoine and DNA. This is in stark contrast to the assumption made by preferential exclusion models, which are often used to interpret the behaviour of compatible solutes within cells and with biomolecules. It is tentatively proposed that the alterations of UV damage to DNA are attributed to ectoine influence on nucleobases through the direct interaction between ectoine and DNA.
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Affiliation(s)
- Marc Benjamin Hahn
- Freie Universität Berlin, Institut für Experimentalphysik, 14195 Berlin, Germany. and Bundesanstalt für Materialforschung und -prüfung (BAM), 12205 Berlin, Germany
| | - Glen J Smales
- Bundesanstalt für Materialforschung und -prüfung (BAM), 12205 Berlin, Germany
| | - Harald Seitz
- Universität Potsdam, Institut für Biochemie und Biologie, 14476 Potsdam, Germany and Fraunhofer Institute for Cell Therapy and Immunology, 14476 Potsdam, Germany
| | - Tihomir Solomun
- Bundesanstalt für Materialforschung und -prüfung (BAM), 12205 Berlin, Germany
| | - Heinz Sturm
- Bundesanstalt für Materialforschung und -prüfung (BAM), 12205 Berlin, Germany
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18
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Shi R, Zhao Z, Liang X, Su Y, Sai L, Zhao J. Structures and vertical detachment energies of water cluster anions (H2O)−n with n = 6–11. Theor Chem Acc 2020. [DOI: 10.1007/s00214-020-2567-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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19
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Svoboda V, Michiels R, LaForge AC, Med J, Stienkemeier F, Slavíček P, Wörner HJ. Real-time observation of water radiolysis and hydrated electron formation induced by extreme-ultraviolet pulses. SCIENCE ADVANCES 2020; 6:eaaz0385. [PMID: 32010776 PMCID: PMC6968931 DOI: 10.1126/sciadv.aaz0385] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 11/26/2019] [Indexed: 05/17/2023]
Abstract
The dominant pathway of radiation damage begins with the ionization of water. Thus far, however, the underlying primary processes could not be conclusively elucidated. Here, we directly study the earliest steps of extreme ultraviolet (XUV)-induced water radiolysis through one-photon excitation of large water clusters using time-resolved photoelectron imaging. Results are presented for H2O and D2O clusters using femtosecond pump pulses centered at 133 or 80 nm. In both excitation schemes, hydrogen or proton transfer is observed to yield a prehydrated electron within 30 to 60 fs, followed by its solvation in 0.3 to 1.0 ps and its decay through geminate recombination on a ∼10-ps time scale. These results are interpreted by comparison with detailed multiconfigurational non-adiabatic ab-initio molecular dynamics calculations. Our results provide the first comprehensive picture of the primary steps of radiation chemistry and radiation damage and demonstrate new approaches for their study with unprecedented time resolution.
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Affiliation(s)
- Vít Svoboda
- Laboratory of Physical Chemistry, ETH-Zürich, 8093 Zürich, Switzerland
| | - Rupert Michiels
- Institute of Physics, University of Freiburg, 79104 Freiburg, Germany
| | - Aaron C. LaForge
- Institute of Physics, University of Freiburg, 79104 Freiburg, Germany
| | - Jakub Med
- Department of Physical chemistry, UCT Prague, 16628 Prague, Czech Republic
| | | | - Petr Slavíček
- Department of Physical chemistry, UCT Prague, 16628 Prague, Czech Republic
| | - Hans Jakob Wörner
- Laboratory of Physical Chemistry, ETH-Zürich, 8093 Zürich, Switzerland
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20
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Ariyarathna IR, Pawłowski F, Ortiz JV, Miliordos E. Aufbau Principle for Diffuse Electrons of Double-Shell Metal Ammonia Complexes: The Case of M(NH3)4@12NH3, M = Li, Be+, B2+. J Phys Chem A 2019; 124:505-512. [DOI: 10.1021/acs.jpca.9b07734] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Isuru R. Ariyarathna
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849-5312, United States
| | - Filip Pawłowski
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849-5312, United States
| | - Joseph Vincent Ortiz
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849-5312, United States
| | - Evangelos Miliordos
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849-5312, United States
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21
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Parobek D, Qiao T, Son DH. Energetic hot electrons from exciton-to-hot electron upconversion in Mn-doped semiconductor nanocrystals. J Chem Phys 2019; 151:120901. [PMID: 31575181 DOI: 10.1063/1.5119398] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Generation of hot electrons and their utilization in photoinduced chemical processes have been the subjects of intense research in recent years mostly exploring hot electrons in plasmonic metal nanostructures created via decay of optically excited plasmon. Here, we present recent progress made in generation and utilization of a different type of hot electrons produced via biphotonic exciton-to-hot electron "upconversion" in Mn-doped semiconductor nanocrystals. Compared to the plasmonic hot electrons, those produced via biphotonic upconversion in Mn-doped semiconductor nanocrystals possess much higher energy, enabling more efficient long-range electron transfer across the high energy barrier. They can even be ejected above the vacuum level creating photoelectrons, which can possibly produce solvated electrons. Despite the biphotonic nature of the upconversion process, hot electrons can be generated with weak cw excitation equivalent to the concentrated solar radiation without requiring intense or high-energy photons. This perspective reviews recent work elucidating the mechanism of generating energetic hot electrons in Mn-doped semiconductor nanocrystals, detection of these hot electrons as photocurrent or photoelectron emission, and their utilization in chemical processes such as photocatalysis. New opportunities that the energetic hot electrons can open by creating solvated electrons, which can be viewed as the longer-lived and mobile version of hot electrons more useful for chemical processes, and the challenges in practical utilization of energetic hot electrons are also discussed.
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Affiliation(s)
- David Parobek
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, USA
| | - Tian Qiao
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, USA
| | - Dong Hee Son
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, USA
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22
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Structure and spectrum of the hydrated electron. A combined quantum chemical statistical mechanical simulation. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.111300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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23
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Kumar A, Becker D, Adhikary A, Sevilla MD. Reaction of Electrons with DNA: Radiation Damage to Radiosensitization. Int J Mol Sci 2019; 20:E3998. [PMID: 31426385 PMCID: PMC6720166 DOI: 10.3390/ijms20163998] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 08/01/2019] [Accepted: 08/12/2019] [Indexed: 01/19/2023] Open
Abstract
This review article provides a concise overview of electron involvement in DNA radiation damage. The review begins with the various states of radiation-produced electrons: Secondary electrons (SE), low energy electrons (LEE), electrons at near zero kinetic energy in water (quasi-free electrons, (e-qf)) electrons in the process of solvation in water (presolvated electrons, e-pre), and fully solvated electrons (e-aq). A current summary of the structure of e-aq, and its reactions with DNA-model systems is presented. Theoretical works on reduction potentials of DNA-bases were found to be in agreement with experiments. This review points out the proposed role of LEE-induced frank DNA-strand breaks in ion-beam irradiated DNA. The final section presents radiation-produced electron-mediated site-specific formation of oxidative neutral aminyl radicals from azidonucleosides and the evidence of radiosensitization provided by these aminyl radicals in azidonucleoside-incorporated breast cancer cells.
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Affiliation(s)
- Anil Kumar
- Department of Chemistry, Oakland University, Rochester, MI 48309, USA
| | - David Becker
- Department of Chemistry, Oakland University, Rochester, MI 48309, USA
| | - Amitava Adhikary
- Department of Chemistry, Oakland University, Rochester, MI 48309, USA
| | - Michael D Sevilla
- Department of Chemistry, Oakland University, Rochester, MI 48309, USA.
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24
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Trinh DTT, Khanitchaidecha W, Channei D, Nakaruk A. Synthesis, characterization and environmental applications of bismuth vanadate. RESEARCH ON CHEMICAL INTERMEDIATES 2019. [DOI: 10.1007/s11164-019-03912-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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25
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Ye M, Iwata K. Ultrafast Electron Solvation in Room Temperature Ionic Liquid Observed by Femtosecond Time-resolved Near-IR Spectroscopy. CHEM LETT 2019. [DOI: 10.1246/cl.181043] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Manping Ye
- College of Optical and Electronic Technology, China Jiliang University, Hangzhou 310018, P. R. China
- Department of Chemistry, Faculty of Science, Gakushuin University, 1-5-1 Mejiro, Toshima-ku, Tokyo 171-8588, Japan
| | - Koichi Iwata
- Department of Chemistry, Faculty of Science, Gakushuin University, 1-5-1 Mejiro, Toshima-ku, Tokyo 171-8588, Japan
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26
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Yang N, Duong CH, Kelleher PJ, McCoy AB, Johnson MA. Deconstructing water's diffuse OH stretching vibrational spectrum with cold clusters. Science 2019; 364:275-278. [PMID: 31000660 DOI: 10.1126/science.aaw4086] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 03/11/2019] [Indexed: 05/05/2023]
Abstract
The diffuse vibrational envelope displayed by water precludes direct observation of how different hydrogen-bond topologies dictate the spectral response of individual hydroxy group (OH) oscillators. Using cold, isotopically labeled cluster ions, we report the spectral signatures of a single, intact water (H2O) molecule embedded at various sites in the clathrate-like cage structure adopted by the Cs+·(D2O)20 ion. These patterns reveal the site-dependent correlation between the frequencies of the two OH groups on the same water molecule and establish that the bound OH companion of the free OH group exclusively accounts for bands in the lower-energy region of the spectrum. The observed multiplet structures reveal the homogeneous linewidths of the fundamentals and quantify the anharmonic contributions arising from coupling to both the intramolecular bending and intermolecular soft modes.
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Affiliation(s)
- Nan Yang
- Sterling Chemistry Laboratory, Yale University, New Haven, CT 06520, USA
| | - Chinh H Duong
- Sterling Chemistry Laboratory, Yale University, New Haven, CT 06520, USA
| | - Patrick J Kelleher
- Sterling Chemistry Laboratory, Yale University, New Haven, CT 06520, USA
| | - Anne B McCoy
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA.
| | - Mark A Johnson
- Sterling Chemistry Laboratory, Yale University, New Haven, CT 06520, USA.
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27
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Wu X, Ehrmaier J, Sobolewski AL, Karsili TNV, Domcke W. Mechanisms of photoreactivity in hydrogen-bonded adenine-H 2O complexes. Phys Chem Chem Phys 2019; 21:14238-14249. [PMID: 30543228 DOI: 10.1039/c8cp05305g] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The mechanisms of photoinduced reactions of adenine with water molecules in hydrogen-bonded adenine-water complexes were investigated with ab initio wave-function-based electronic-structure calculations. Two excited-state electron/proton transfer reaction mechanisms have been characterized: H-atom abstraction from water by photoexcited adenine as well as H-atom transfer from photoexcited adenine or the (adenine+H) radical to water. In the water-to-adenine H-atom transfer reaction, an electron from one of the p orbitals of the water molecule fills the hole in the n (π) orbital of the nπ* (ππ*) excited state of adenine, resulting in a charge-separated electronic state. The electronic charge separation is neutralized by the transfer of a proton from the water molecule to adenine, resulting in the (adenine+H)OH biradical in the electronic ground state. In the adenine-to-water H-atom transfer reaction, πσ* states localized at the acidic sites of adenine provide the mechanism for the photoejection of an electron from adenine, which is followed by proton transfer to the hydrogen-bonded water molecule, resulting in the (adenine-H)H3O biradical. The energy profiles of the photoreactions have been computed as relaxed scans with the ADC(2) electronic-structure method. These reactions, which involve the reactivity of adenine with hydrogen-bonded water molecules, compete with the well-established intrinsic excited-state deactivation mechanisms of adenine via ring-puckering or ring-opening conical intersections. By providing additional decay channels, the electron/proton exchange reactions with water can account for the observed significantly shortened excited-state lifetime of adenine in aqueous environments. These findings indicate that adenine possibly was not only a photostabilizer at the beginning of life, but also a primordial photocatalyst for water splitting.
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Affiliation(s)
- Xiuxiu Wu
- Department of Chemistry, Technical University of Munich, D-85747 Garching, Germany.
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28
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Abstract
A cavity or excluded-volume structure best explains the experimental properties of the aqueous or “hydrated” electron.
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Affiliation(s)
- John M. Herbert
- Department of Chemistry & Biochemistry
- The Ohio State University
- Columbus
- USA
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29
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Smith ME, Green NJB, Pimblott SM. Methods for the Simulation of the Slowing of Low-Energy Electrons in Water. J Comput Chem 2018; 39:2217-2225. [PMID: 30238486 DOI: 10.1002/jcc.25536] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 06/29/2018] [Accepted: 06/29/2018] [Indexed: 11/08/2022]
Abstract
A computational Monte Carlo simulation approach for modeling the thermalization of low-energy electrons is presented. The simulation methods rely on, and use, experimentally based cross sections for elastic and inelastic collisions. To demonstrate the different simulation options, average numbers of interactions and the range of low-energy electrons with initial energies ranging from 1 to 20 eV are calculated for density normalized gaseous water. Experimental gas-phase cross sections for (subexcitation) electrons of energies in the range of 1-20 eV were taken from the compilation of Hayashi. The ballistic collision-by-collision simulations provide information on the intricacies of the thermalization processes not available experimentally. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Marisa E Smith
- Dalton Cumbrian Facility, West Lakes Science and Technology Park, Moor Row, CA24 3HA, United Kingdom.,School of Chemistry, The University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom
| | - N J B Green
- Department of Physical & Theoretical Chemistry, Oxford University, Oxford, OX1 3PA, United Kingdom
| | - S M Pimblott
- Dalton Cumbrian Facility, West Lakes Science and Technology Park, Moor Row, CA24 3HA, United Kingdom.,School of Chemistry, The University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom.,Nuclear Science User Facilities, Idaho National Laboratory, Idaho Falls, Idaho, IDA3415
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30
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Hahn MB, Meyer S, Schröter MA, Seitz H, Kunte HJ, Solomun T, Sturm H. Direct electron irradiation of DNA in a fully aqueous environment. Damage determination in combination with Monte Carlo simulations. Phys Chem Chem Phys 2018; 19:1798-1805. [PMID: 28059422 DOI: 10.1039/c6cp07707b] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
We report on a study in which plasmid DNA in water was irradiated with 30 keV electrons generated by a scanning electron microscope and passed through a 100 nm thick Si3N4 membrane. The corresponding Monte Carlo simulations suggest that the kinetic energy spectrum of the electrons throughout the water is dominated by low energy electrons (<100 eV). The DNA radiation damage, single-strand breaks (SSBs) and double-strand breaks (DSBs), was determined by gel electrophoresis. The median lethal dose of D1/2 = 1.7 ± 0.3 Gy was found to be much smaller as compared to partially or fully hydrated DNA irradiated under vacuum conditions. The ratio of the DSBs to SSBs was found to be 1 : 12 as compared to 1 : 88 found for hydrated DNA. Our method enables quantitative measurements of radiation damage to biomolecules (DNA, proteins) in solutions under varying conditions (pH, salinity, co-solutes) for an electron energy range which is difficult to probe by standard methods.
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Affiliation(s)
- Marc Benjamin Hahn
- Free University Berlin, Department of Physics, D-14195 Berlin, Germany. and Bundesanstalt für Materialforschung und Prüfung, D-12205 Berlin, Germany.
| | - Susann Meyer
- Bundesanstalt für Materialforschung und Prüfung, D-12205 Berlin, Germany. and University of Potsdam, Institute of Biochemistry and Biology, D-14476 Potsdam, Germany
| | | | - Harald Seitz
- Fraunhofer-Institut für Zelltherapie und Immunologie, Institutsteil Bioanalytik und Bioprozesse, D-14476 Potsdam, Germany
| | - Hans-Jörg Kunte
- Bundesanstalt für Materialforschung und Prüfung, D-12205 Berlin, Germany.
| | - Tihomir Solomun
- Bundesanstalt für Materialforschung und Prüfung, D-12205 Berlin, Germany.
| | - Heinz Sturm
- Bundesanstalt für Materialforschung und Prüfung, D-12205 Berlin, Germany. and Technical University Berlin, D-10587 Berlin, Germany
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31
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Pshenichnyuk SA, Modelli A, Komolov AS. Interconnections between dissociative electron attachment and electron-driven biological processes. INT REV PHYS CHEM 2018. [DOI: 10.1080/0144235x.2018.1461347] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Stanislav A. Pshenichnyuk
- Institute of Molecule and Crystal Physics – Subdivision of the Ufa Research Centre of the Russian Academy of Sciences, Ufa, Russia
| | - Alberto Modelli
- Dipartimento di Chimica ‘G. Ciamician’, Università di Bologna, Bologna, Italy
- Centro Interdipartimentale di Ricerca in Scienze Ambientali, Ravenna, Italy
| | - Alexei S. Komolov
- Department of Solid State Electronics, St. Petersburg State University, St. Petersburg, Russia
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32
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Riley JW, Wang B, Woodhouse JL, Assmann M, Worth GA, Fielding HH. Unravelling the Role of an Aqueous Environment on the Electronic Structure and Ionization of Phenol Using Photoelectron Spectroscopy. J Phys Chem Lett 2018; 9:678-682. [PMID: 29356540 DOI: 10.1021/acs.jpclett.7b03310] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Water is the predominant medium for chemistry and biology, yet its role in determining how molecules respond to ultraviolet light is not well understood at the molecular level. Here, we combine gas-phase and liquid-microjet photoelectron spectroscopy to investigate how an aqueous environment influences the electronic structure and relaxation dynamics of phenol, a ubiquitous motif in many biologically relevant chromophores. The vertical ionization energies of electronically excited states are important quantities that govern the rates of charge-transfer reactions, and, in phenol, the vertical ionization energy of the first electronically excited state is found to be lowered by around 0.8 eV in aqueous solution. The initial relaxation dynamics following photoexcitation with ultraviolet light appear to be remarkably similar in the gas-phase and aqueous solution; however, in aqueous solution, we find evidence to suggest that solvated electrons are formed on an ultrafast time scale following photoexcitation just above the conical intersection between the first two excited electronic states.
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Affiliation(s)
- Jamie W Riley
- Department of Chemistry, University College London , 20 Gordon Street, London, WC1H 0AJ, United Kingdom
| | - Bingxing Wang
- Department of Chemistry, University College London , 20 Gordon Street, London, WC1H 0AJ, United Kingdom
| | - Joanne L Woodhouse
- Department of Chemistry, University College London , 20 Gordon Street, London, WC1H 0AJ, United Kingdom
| | - Mariana Assmann
- Department of Chemistry, University College London , 20 Gordon Street, London, WC1H 0AJ, United Kingdom
| | - Graham A Worth
- Department of Chemistry, University College London , 20 Gordon Street, London, WC1H 0AJ, United Kingdom
| | - Helen H Fielding
- Department of Chemistry, University College London , 20 Gordon Street, London, WC1H 0AJ, United Kingdom
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33
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Liu G, Landry C, Ghandi K. Prediction of rate constants of important chemical reactions in water radiation chemistry in sub and supercritical water – non-equilibrium reactions. CAN J CHEM 2018. [DOI: 10.1139/cjc-2017-0315] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The rate constants for reactions involved in the radiolysis of water under relevant thermodynamic conditions in supercritical water-cooled reactors are estimated for inputs in simulations of the radiation chemistry in Generation IV nuclear reactors. We have discussed the mechanism of each chemical reaction with a focus on non-equilibrium reactions. We found most of the reactions are activation controlled above the critical point and that the rate constants are not significantly pressure dependent below 300 °C. This work will aid industry with developing chemical control strategies to suppress the concentration of eroding species.
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Affiliation(s)
- Guangdong Liu
- Department of Physics, Mount Allison University, Sackville, NB E4L 1E2, Canada
| | - Cody Landry
- Department of Chemistry and Biochemistry, Mount Allison University, Sackville, NB E4L 1E2, Canada
| | - Khashayar Ghandi
- Department of Physics, Mount Allison University, Sackville, NB E4L 1E2, Canada
- Department of Chemistry and Biochemistry, Mount Allison University, Sackville, NB E4L 1E2, Canada
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34
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Gaiduk AP, Pham TA, Govoni M, Paesani F, Galli G. Electron affinity of liquid water. Nat Commun 2018; 9:247. [PMID: 29339731 PMCID: PMC5770385 DOI: 10.1038/s41467-017-02673-z] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 12/15/2017] [Indexed: 11/09/2022] Open
Abstract
Understanding redox and photochemical reactions in aqueous environments requires a precise knowledge of the ionization potential and electron affinity of liquid water. The former has been measured, but not the latter. We predict the electron affinity of liquid water and of its surface from first principles, coupling path-integral molecular dynamics with ab initio potentials, and many-body perturbation theory. Our results for the surface (0.8 eV) agree well with recent pump-probe spectroscopy measurements on amorphous ice. Those for the bulk (0.1-0.3 eV) differ from several estimates adopted in the literature, which we critically revisit. We show that the ionization potential of the bulk and surface are almost identical; instead their electron affinities differ substantially, with the conduction band edge of the surface much deeper in energy than that of the bulk. We also discuss the significant impact of nuclear quantum effects on the fundamental gap and band edges of the liquid.
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Affiliation(s)
- Alex P Gaiduk
- Institute for Molecular Engineering, The University of Chicago, Chicago, IL, 60637, USA
| | - Tuan Anh Pham
- Lawrence Livermore National Laboratory, Livermore, CA, 94551, USA
| | - Marco Govoni
- Institute for Molecular Engineering, The University of Chicago, Chicago, IL, 60637, USA.,Materials Science Division, Argonne National Laboratory, Argonne, IL, 60439, USA
| | - Francesco Paesani
- Department of Chemistry and Biochemistry, Materials Science and Engineering, San Diego Supercomputer Center, University of California, San Diego, 92093, USA.
| | - Giulia Galli
- Institute for Molecular Engineering, The University of Chicago, Chicago, IL, 60637, USA. .,Materials Science Division, Argonne National Laboratory, Argonne, IL, 60439, USA.
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35
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Cheung KP, Veksler D, Campbell JP. Local field effect on charge-capture/emission dynamics. IEEE TRANSACTIONS ON ELECTRON DEVICES 2017; 64:5099-5016. [PMID: 29375150 PMCID: PMC5783311 DOI: 10.1109/ted.2017.2764804] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Charge-capture/emission is ubiquitous in electron devices. Its dynamics often play critical roles in device operation and reliability. Treatment of this basic process is found in many text books and is considered well understood. As in many electron device models, the individuality of immobile charge is commonly replaced with the average quantity of charge density. This has worked remarkably well when large numbers of individual charges (ensemble) are involved. As device geometries become very small, the ensemble "averaging" becomes far less accurate. In this work, the charge-capture/emission dynamic of Metal-Oxide-Semiconductor-Field-Effect-Transistor (MOSFET) is re-examined with full consideration of individual charges and the local field in their immediate vicinity. A dramatic modification of the local band diagram resulted, forcing a drastic change in emission mechanism. The implication is that many well-understood phenomena involving charge capture/emission will need to be reconsidered. As an example, this new picture is applied to the random telegraph noise (RTN) phenomenon. When the screening of a trapped charge by a polar medium such as SiO2 is quantitatively accounted for in this local field picture, a new physically sound RTN emission mechanism emerges. Similarly, the dynamics of post-stress recovery of Negative-Bias-Instability of p-channel MOSFET can be more rationally explained.
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Affiliation(s)
- Kin P Cheung
- Engineering Physics Division, National Institute of Standards and Technology, Gaithersburg, MD 20899 USA
| | - Dmitry Veksler
- Engineering Physics Division, National Institute of Standards and Technology, Gaithersburg, MD 20899 USA
| | - Jason P Campbell
- Engineering Physics Division, National Institute of Standards and Technology, Gaithersburg, MD 20899 USA
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36
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Verkhovtsev A, Ellis-Gibbings L, Blanco F, García G. Interference effects in electron scattering from small water clusters. Chem Phys Lett 2017. [DOI: 10.1016/j.cplett.2017.07.052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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37
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Affiliation(s)
- John M. Herbert
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210
| | - Marc P. Coons
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210
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38
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Jiao Y, Adams B, Rose-Petruck C. Ultrafast X-ray measurements of the glass-like, high-frequency stiffness of aqueous solutions. Phys Chem Chem Phys 2017; 19:21095-21100. [DOI: 10.1039/c7cp02747h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The ultrafast dynamics of the domains surrounding solutes in aqueous solution were measured using laser-generating GHz phonons in 30 mM ferrocyanide solutions and the resulting molecular motions of the solutes and their hydrogen-bonded solvation shells were detected using ultrafast X-ray absorption spectroscopy (UXAS).
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Affiliation(s)
- Yishuo Jiao
- Department of Chemistry
- Brown University
- Providence
- USA
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39
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Pshenichnyuk SA, Modelli A, Lazneva EF, Komolov AS. Role of Resonance Electron Attachment in Phytoremediation of Halogenated Herbicides. J Phys Chem B 2016; 120:12098-12104. [DOI: 10.1021/acs.jpcb.6b10149] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Stanislav A. Pshenichnyuk
- Institute
of Molecule and Crystal Physics, Ufa Research Centre, Russian Academy of Sciences, Prospeκt Oktyabrya 151, 450075 Ufa, Russia
- St. Petersburg State University, Universitetskaya nab. 7/9, 199034 St. Petersburg, Russia
| | - Alberto Modelli
- Dipartimento
di Chimica “G. Ciamician”, Università di Bologna, via Selmi 2, 40126 Bologna, Italy
- Centro Interdipartimentale di Ricerca in Scienze Ambientali, via S. Alberto 163, 48123 Ravenna, Italy
| | - Eleonora F. Lazneva
- St. Petersburg State University, Universitetskaya nab. 7/9, 199034 St. Petersburg, Russia
| | - Alexei S. Komolov
- St. Petersburg State University, Universitetskaya nab. 7/9, 199034 St. Petersburg, Russia
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40
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Coons MP, You ZQ, Herbert JM. The Hydrated Electron at the Surface of Neat Liquid Water Appears To Be Indistinguishable from the Bulk Species. J Am Chem Soc 2016; 138:10879-86. [DOI: 10.1021/jacs.6b06715] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Marc P. Coons
- Department of Chemistry and
Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Zhi-Qiang You
- Department of Chemistry and
Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - John M. Herbert
- Department of Chemistry and
Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
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41
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Zhang C, Bu Y. Benchmark calculations of excess electrons in water cluster cavities: balancing the addition of atom-centered diffuse functions versus floating diffuse functions. Phys Chem Chem Phys 2016; 18:23812-21. [PMID: 27522987 DOI: 10.1039/c6cp04224d] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Diffuse functions have been proved to be especially crucial for the accurate characterization of excess electrons which are usually bound weakly in intermolecular zones far away from the nuclei. To examine the effects of diffuse functions on the nature of the cavity-shaped excess electrons in water cluster surroundings, both the HOMO and LUMO distributions, vertical detachment energies (VDEs) and visible absorption spectra of two selected (H2O)24(-) isomers are investigated in the present work. Two main types of diffuse functions are considered in calculations including the Pople-style atom-centered diffuse functions and the ghost-atom-based floating diffuse functions. It is found that augmentation of atom-centered diffuse functions contributes to a better description of the HOMO (corresponding to the VDE convergence), in agreement with previous studies, but also leads to unreasonable diffuse characters of the LUMO with significant red-shifts in the visible spectra, which is against the conventional point of view that the more the diffuse functions, the better the results. The issue of designing extra floating functions for excess electrons has also been systematically discussed, which indicates that the floating diffuse functions are necessary not only for reducing the computational cost but also for improving both the HOMO and LUMO accuracy. Thus, the basis sets with a combination of partial atom-centered diffuse functions and floating diffuse functions are recommended for a reliable description of the weakly bound electrons. This work presents an efficient way for characterizing the electronic properties of weakly bound electrons accurately by balancing the addition of atom-centered diffuse functions and floating diffuse functions and also by balancing the computational cost and accuracy of the calculated results, and thus is very useful in the relevant calculations of various solvated electron systems and weakly bound anionic systems.
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Affiliation(s)
- Changzhe Zhang
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, 250100, P. R. China.
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42
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Akhgarnusch A, Tang WK, Zhang H, Siu CK, Beyer MK. Charge transfer reactions between gas-phase hydrated electrons, molecular oxygen and carbon dioxide at temperatures of 80-300 K. Phys Chem Chem Phys 2016; 18:23528-37. [PMID: 27498686 DOI: 10.1039/c6cp03324e] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The recombination reactions of gas-phase hydrated electrons (H2O)n˙(-) with CO2 and O2, as well as the charge exchange reaction of CO2˙(-)(H2O)n with O2, were studied by Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry in the temperature range T = 80-300 K. Comparison of the rate constants with collision models shows that CO2 reacts with 50% collision efficiency, while O2 reacts considerably slower. Nanocalorimetry yields internally consistent results for the three reactions. Converted to room temperature condensed phase, this yields hydration enthalpies of CO2˙(-) and O2˙(-), ΔHhyd(CO2˙(-)) = -334 ± 44 kJ mol(-1) and ΔHhyd(O2˙(-)) = -404 ± 28 kJ mol(-1). Quantum chemical calculations show that the charge exchange reaction proceeds via a CO4˙(-) intermediate, which is consistent with a fully ergodic reaction and also with the small efficiency. Ab initio molecular dynamics simulations corroborate this picture and indicate that the CO4˙(-) intermediate has a lifetime significantly above the ps regime.
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Affiliation(s)
- Amou Akhgarnusch
- Institut für Physikalische Chemie, Christian-Albrechts-Universität zu Kiel, Olshausenstrasse 40, 24098 Kiel, Germany
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43
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Reinhardt CR, Jaglinski TC, Kastenschmidt AM, Song EH, Gross AK, Krause AJ, Gollmar JM, Meise KJ, Stenerson ZS, Weibel TJ, Dison A, Finnegan MR, Griesi DS, Heltne MD, Hughes TG, Hunt CD, Jansen KA, Xiong AH, Hati S, Bhattacharyya S. Insight into the kinetics and thermodynamics of the hydride transfer reactions between quinones and lumiflavin: a density functional theory study. J Mol Model 2016; 22:199. [PMID: 27491848 DOI: 10.1007/s00894-016-3074-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Accepted: 07/17/2016] [Indexed: 12/14/2022]
Abstract
The kinetics and equilibrium of the hydride transfer reaction between lumiflavin and a number of substituted quinones was studied using density functional theory. The impact of electron withdrawing/donating substituents on the redox potentials of quinones was studied. In addition, the role of these substituents on the kinetics of the hydride transfer reaction with lumiflavin was investigated in detail under the transition state (TS) theory assumption. The hydride transfer reactions were found to be more favorable for an electron-withdrawing substituent. The activation barrier exhibited a quadratic relationship with the driving force of these reactions as derived under the formalism of modified Marcus theory. The present study found a significant extent of electron delocalization in the TS that is stabilized by enhanced electrostatic, polarization, and exchange interactions. Analysis of geometry, bond-orders, and energetics revealed a predominant parallel (Leffler-Hammond) effect on the TS. Closer scrutiny reveals that electron-withdrawing substituents, although located on the acceptor ring, reduce the N-H bond order of the donor fragment in the precursor complex. Carried out in the gas-phase, this is the first ever report of a theoretical study of flavin's hydride transfer reactions with quinones, providing an unfiltered view of the electronic effect on the nuclear reorganization of donor-acceptor complexes.
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Affiliation(s)
- Clorice R Reinhardt
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, WI, 54702, USA
| | - Tanner C Jaglinski
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, WI, 54702, USA
| | - Ashly M Kastenschmidt
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, WI, 54702, USA
| | - Eun H Song
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, WI, 54702, USA
| | - Adam K Gross
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, WI, 54702, USA
| | - Alyssa J Krause
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, WI, 54702, USA
| | - Jonathan M Gollmar
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, WI, 54702, USA
| | - Kristin J Meise
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, WI, 54702, USA
| | - Zachary S Stenerson
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, WI, 54702, USA
| | - Tyler J Weibel
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, WI, 54702, USA
| | - Andrew Dison
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, WI, 54702, USA
| | - Mackenzie R Finnegan
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, WI, 54702, USA
| | - Daniel S Griesi
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, WI, 54702, USA
| | - Michael D Heltne
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, WI, 54702, USA
| | - Tom G Hughes
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, WI, 54702, USA
| | - Connor D Hunt
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, WI, 54702, USA
| | - Kayla A Jansen
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, WI, 54702, USA
| | - Adam H Xiong
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, WI, 54702, USA
| | - Sanchita Hati
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, WI, 54702, USA
| | - Sudeep Bhattacharyya
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, WI, 54702, USA.
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44
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Kumar A, Walker JA, Bartels DM, Sevilla MD. A Simple ab Initio Model for the Hydrated Electron That Matches Experiment. J Phys Chem A 2016; 119:9148-59. [PMID: 26275103 DOI: 10.1021/acs.jpca.5b04721] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Since its discovery over 50 years ago, the "structure" and properties of the hydrated electron have been a subject for wonderment and also fierce debate. In the present work we seriously explore a minimal model for the aqueous electron, consisting of a small water anion cluster embedded in a polarized continuum, using several levels of ab initio calculation and basis set. The minimum energy "zero Kelvin" structure found for any 4-water (or larger) anion cluster, at any post-Hartree–Fock theory level, is very similar to a recently reported embedded-DFT-in-classical-water-MD simulation (Uhlig, Marsalek, and Jungwirth, J. Phys. Chem. Lett. 2012, 3, 3071−3075), with four OH bonds oriented toward the maximum charge density in a small central "void". The minimum calculation with just four water molecules does a remarkably good job of reproducing the resonance Raman properties, the radius of gyration derived from the optical spectrum, the vertical detachment energy, and the hydration free energy. For the first time we also successfully calculate the EPR g-factor and (low temperature ice) hyperfine couplings. The simple tetrahedral anion cluster model conforms very well to experiment, suggesting it does in fact represent the dominant structural motif of the hydrated electron.
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45
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Pshenichnyuk SA, Modelli A, Lazneva EF, Komolov AS. Hypothesis for the Mechanism of Ascorbic Acid Activity in Living Cells Related to Its Electron-Accepting Properties. J Phys Chem A 2016; 120:2667-76. [DOI: 10.1021/acs.jpca.6b02272] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Stanislav A. Pshenichnyuk
- Institute of Molecule and Crystal Physics,
Ufa Research Centre, Russian Academy of Sciences, Prospekt Oktyabrya
151, 450075 Ufa, Russia
- Physics Faculty, St. Petersburg State University, Uljanovskaja 1, 198504 St. Petersburg, Russia
| | - Alberto Modelli
- Dipartimento
di Chimica “G. Ciamician”, Università di Bologna, via Selmi 2, 40126 Bologna, Italy
- Centro Interdipartimentale di Ricerca in Scienze Ambientali, via S. Alberto 163, 48123 Ravenna, Italy
| | - Eleonora F. Lazneva
- Physics Faculty, St. Petersburg State University, Uljanovskaja 1, 198504 St. Petersburg, Russia
| | - Alexei S. Komolov
- Physics Faculty, St. Petersburg State University, Uljanovskaja 1, 198504 St. Petersburg, Russia
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46
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Krishtal A, Pavanello M. Revealing electronic open quantum systems with subsystem TDDFT. J Chem Phys 2016; 144:124118. [PMID: 27036438 DOI: 10.1063/1.4944526] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Open quantum systems (OQSs) are perhaps the most realistic systems one can approach through simulations. In recent years, describing OQSs with Density Functional Theory (DFT) has been a prominent avenue of research with most approaches based on a density matrix partitioning in conjunction with an ad-hoc description of system-bath interactions. We propose a different theoretical approach to OQSs based on partitioning of the electron density. Employing the machinery of subsystem DFT (and its time-dependent extension), we provide a novel way of isolating and analyzing the various terms contributing to the coupling between the system and the surrounding bath. To illustrate the theory, we provide numerical simulations on a toy system (a molecular dimer) and on a condensed phase system (solvated excimer). The simulations show that non-Markovian dynamics in the electronic system-bath interactions are important in chemical applications. For instance, we show that the superexchange mechanism of transport in donor-bridge-acceptor systems is a non-Markovian interaction between the donor-acceptor (OQS) with the bridge (bath) which is fully characterized by real-time subsystem time-dependent DFT.
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Affiliation(s)
- Alisa Krishtal
- Department of Chemistry, Rutgers University, Newark, New Jersey 07102, USA
| | - Michele Pavanello
- Department of Chemistry, Rutgers University, Newark, New Jersey 07102, USA
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47
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Pshenichnyuk SA, Elkin YN, Kulesh NI, Lazneva EF, Komolov AS. Low-energy electron interaction with retusin extracted from Maackia amurensis: towards a molecular mechanism of the biological activity of flavonoids. Phys Chem Chem Phys 2016; 17:16805-12. [PMID: 26058603 DOI: 10.1039/c5cp02890f] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The antioxidant isoflavone retusin efficiently attaches low-energy electrons in vacuo, generating fragment species via dissociative electron attachment (DEA), as has been shown by DEA spectroscopy. According to in silico results obtained by means of density functional theory, retusin is able to attach solvated electrons and could be decomposed under reductive conditions in vivo, for instance, near the mitochondrial electron transport chain, analogous to gas-phase DEA. The most intense decay channels of retusin temporary negative ions were found to be associated with the elimination of H atoms and H2 molecules. Doubly dehydrogenated fragment anions were predicted to possess a quinone structure. It is thought that molecular hydrogen, known for its selective antioxidant properties, can be efficiently generated via electron attachment to retusin in mitochondria and may be responsible for its antioxidant activity. The second abundant species, i.e., quinone bearing an excess negative charge, can serve as an electron carrier and can return the captured electron back to the respiration cycle. The number of OH substituents and their relative positions are crucial for the present molecular mechanism, which can explain the radical scavenging activity of polyphenolic compounds.
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Affiliation(s)
- Stanislav A Pshenichnyuk
- Institute of Molecule and Crystal Physics, Ufa Research Centre, Russian Academy of Sciences, Prospect Oktyabrya 151, 450075 Ufa, Russia.
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48
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Wang S, Zhao P, Zhang C, Bu Y. The Equally Important Role of Adenine Derivatives to That of Pyrimidine Derivatives in Near‐0 eV Electron‐Induced DNA Lesions. Chemphyschem 2016; 17:1669-77. [DOI: 10.1002/cphc.201600002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Indexed: 01/27/2023]
Affiliation(s)
- Shoushan Wang
- Institute of Theoretical Chemistry School of Chemistry and Chemical Engineering Shandong University Jinan 250100 P. R. China
| | - Peiwen Zhao
- Institute of Theoretical Chemistry School of Chemistry and Chemical Engineering Shandong University Jinan 250100 P. R. China
| | - Changzhe Zhang
- Institute of Theoretical Chemistry School of Chemistry and Chemical Engineering Shandong University Jinan 250100 P. R. China
| | - Yuxiang Bu
- Institute of Theoretical Chemistry School of Chemistry and Chemical Engineering Shandong University Jinan 250100 P. R. China
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49
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Kumar A, Adhikary A, Shamoun L, Sevilla MD. Do Solvated Electrons (e(aq)⁻) Reduce DNA Bases? A Gaussian 4 and Density Functional Theory-Molecular Dynamics Study. J Phys Chem B 2016; 120:2115-23. [PMID: 26878197 PMCID: PMC4863935 DOI: 10.1021/acs.jpcb.5b11269] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The solvated electron (e(aq)⁻) is a primary intermediate after an ionization event that produces reductive DNA damage. Accurate standard redox potentials (E(o)) of nucleobases and of e(aq)⁻ determine the extent of reaction of e(aq)⁻ with nucleobases. In this work, E(o) values of e(aq)⁻ and of nucleobases have been calculated employing the accurate ab initio Gaussian 4 theory including the polarizable continuum model (PCM). The Gaussian 4-calculated E(o) of e(aq)⁻ (-2.86 V) is in excellent agreement with the experimental one (-2.87 V). The Gaussian 4-calculated E(o) of nucleobases in dimethylformamide (DMF) lie in the range (-2.36 V to -2.86 V); they are in reasonable agreement with the experimental E(o) in DMF and have a mean unsigned error (MUE) = 0.22 V. However, inclusion of specific water molecules reduces this error significantly (MUE = 0.07). With the use of a model of e(aq)⁻ nucleobase complex with six water molecules, the reaction of e(aq)⁻ with the adjacent nucleobase is investigated using approximate ab initio molecular dynamics (MD) simulations including PCM. Our MD simulations show that e(aq)⁻ transfers to uracil, thymine, cytosine, and adenine, within 10 to 120 fs and e(aq)⁻ reacts with guanine only when a water molecule forms a hydrogen bond to O6 of guanine which stabilizes the anion radical.
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Affiliation(s)
- Anil Kumar
- Department of Chemistry, Oakland University , Rochester, Michigan 48309, United States
| | - Amitava Adhikary
- Department of Chemistry, Oakland University , Rochester, Michigan 48309, United States
| | - Lance Shamoun
- Department of Chemistry, Oakland University , Rochester, Michigan 48309, United States
| | - Michael D Sevilla
- Department of Chemistry, Oakland University , Rochester, Michigan 48309, United States
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50
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Wang S, Zhao P, Zhang C, Bu Y. Mechanisms Responsible for High Energy Radiation Induced Damage to Single-Stranded DNA Modified by Radiosensitizing 5-Halogenated Deoxyuridines. J Phys Chem B 2016; 120:2649-57. [PMID: 26913546 DOI: 10.1021/acs.jpcb.5b11432] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Experimental studies showed that high energy radiation induced base release and DNA backbone breaks mainly occur at the neighboring 5' nucleotide when a single-stranded DNA is modified by radiosensitizing 5-halogenated deoxyuridines. However, no mechanism can be used to interpret these experimental observations. To better understand the radiosensitivity of 5-halogenated deoxyuridines, mechanisms involving hydrogen abstraction by the uracil-5-yl radical from the C2' and C3' positions of an adjacent nucleotide separately followed by the C3'-O3' or N-glycosidic bond rupture and the P-O3' bond breakage are investigated in the DNA sequence 5'-TU(•)-3' employing density functional theory calculations in the present study. It is found that hydrogen abstractions from both positions are comparable with the one from the C2' site slightly more favorable. The N-glycosidic bond cleavage in the neighboring 5' nucleotide following the internucleotide C2'-Ha abstraction is estimated to have the lowest activation free energies, indicating that the adjacent 5' base release dominates electron induced damage to single-stranded DNA incorporated by 5-halogenated deoxyuridines. Relative to the P-O3' bond breakage after the internucleotide C3'-H abstraction, the C3'-O3' bond rupture in the neighboring 5' nucleotide following the internucleotide C2'-Ha abstraction is predicted to have a lower activation free energy, implying that single-stranded DNA backbone breaks are prone to occur at the C3'-O3' bond site. The 5'-TU(•)-3' species has substantial electron affinity and can even capture a hydrated electron, forming the 5'-TU(-)-3' anion. However, the electron induced C3'-O3' bond rupture in 5'-TU(-)-3' anion via a pathway of internucleotide proton abstraction is only minor in both the gas phase and aqueous solution. The present theoretical predictions can interpret rationally experimental observations, thereby demonstrating that the mechanisms proposed here are responsible for high energy radiation induced damage to single-stranded DNA incorporated by radiosensitizing 5-halogenated deoxyuridines. By comparing with previous results, our work proves that the radiosensitizing action of 5-bromo-2-deoxyuridine is not weaker but stronger than its isomer 6-bromo-2-deoxyuridine on the basis of the available data.
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Affiliation(s)
- Shoushan Wang
- School of Chemistry and Chemical Engineering, Institute of Theoretical Chemistry, Shandong University , Jinan 250100, P. R. China
| | - Peiwen Zhao
- School of Chemistry and Chemical Engineering, Institute of Theoretical Chemistry, Shandong University , Jinan 250100, P. R. China
| | - Changzhe Zhang
- School of Chemistry and Chemical Engineering, Institute of Theoretical Chemistry, Shandong University , Jinan 250100, P. R. China
| | - Yuxiang Bu
- School of Chemistry and Chemical Engineering, Institute of Theoretical Chemistry, Shandong University , Jinan 250100, P. R. China
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