1
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Siddiki MAKA, Kumar K, Singh H, Mukherjee J, Tribedi LC, Misra D. Charge-symmetric and -asymmetric fragmentation dynamics of argon dimers in slow Ar8+-Ar2 collisions. J Chem Phys 2024; 160:224304. [PMID: 38856070 DOI: 10.1063/5.0209104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 05/27/2024] [Indexed: 06/11/2024] Open
Abstract
We present an experimental study of multiple-electron capture-induced fragmentation dynamics of Ar2m+ (4 ≤m≤ 7) dimer ions in 4 keV/u Ar8+-Ar2 collisions. The fragment recoil ion pairs and the charge-changing projectiles are coincidentally measured using a double coincidence technique. The branching ratios between the different charge-sharing fragmentation channels show an inherent enhancement of the asymmetric channels. The kinetic energy release (KER) distributions for the associated electron capture process show a shift in the mean KER values toward the higher side with increasing capture stabilization. The interplay between the different projectile autoionization processes sheds light on the energy depositions to the system during collisions. The Coulomb potential energy curves give a physical insight into the role of the projectile final states in the dimer fragmentation dynamics. The dimer-axis orientation-dependent cross sections for the asymmetric fragmentation channels reveal a forward-backward asymmetry that arises from the geometry of the collision system. Our findings thus give insight into the impact parameter-controlled fragmentation dynamics of multiply charged Ar2m+ dimer ions in highly charged ion-dimer slow collisions.
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Affiliation(s)
- Md Abul Kalam Azad Siddiki
- Department of Nuclear and Atomic Physics, Tata Institute of Fundamental Research, Dr. Homi Bhabha Road, Colaba, Mumbai 400005, India
| | - Kamal Kumar
- Department of Nuclear and Atomic Physics, Tata Institute of Fundamental Research, Dr. Homi Bhabha Road, Colaba, Mumbai 400005, India
| | - Harpreet Singh
- Department of Nuclear and Atomic Physics, Tata Institute of Fundamental Research, Dr. Homi Bhabha Road, Colaba, Mumbai 400005, India
| | - Jibak Mukherjee
- Department of Nuclear and Atomic Physics, Tata Institute of Fundamental Research, Dr. Homi Bhabha Road, Colaba, Mumbai 400005, India
| | - Lokesh C Tribedi
- Department of Nuclear and Atomic Physics, Tata Institute of Fundamental Research, Dr. Homi Bhabha Road, Colaba, Mumbai 400005, India
| | - Deepankar Misra
- Department of Nuclear and Atomic Physics, Tata Institute of Fundamental Research, Dr. Homi Bhabha Road, Colaba, Mumbai 400005, India
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2
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Kundu N, Nandi D. Observation of Renner-Teller and predissociation coupled vibronic intensity borrowing in dissociative electron attachment to OCS. J Chem Phys 2024; 160:114315. [PMID: 38506287 DOI: 10.1063/5.0188833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 02/27/2024] [Indexed: 03/21/2024] Open
Abstract
We use a time-of-flight-based velocity map imaging method to look into the dissociative electron attachment to a linear OCS molecule at electron beam energies ranging from 4.5 to 8.5 eV. The conical time-gated wedge slice imaging method is utilized to extract fragments' slice images, kinetic energy (KE), and angular distributions, which provide a complete kinematic understanding of this experiment on the dissociative electron attachment process. We observe that the formation of S- is relatively higher than the O- product. Three distinct dissociative KE bands of S-/OCS have been observed for the 5.0 and 6.5 eV resonance positions. We notice a prominent rovibrationally coupled bimodality for each KE band in the variation of the most probable KE values. When the electron energy is changed from 5.5 to 6.0 eV, we observed vibronic intensity borrowing in the highest momentum band of S- via the Σ → Π symmetric dipole-forbidden transitions within the 1.5 eV energy gap. Multiple peaks in the angular distributions of S- and their modeling indicate the presence of Renner-Teller vibronic splitting. Using Q-Chem's implemented complex absorbing potential-equation of motion-electron affinity coupled cluster singles and doubles aug-cc-pVDZ+4s3p level of multireference-based electronic structure theory, we confirm the presence of OCS temporary negative ion bending vibrations and Renner-Teller vibronic splittings for the Π symmetric states. Additionally, we notice the presence of a non-radiative predissociation continuum (bringing down the rotational spectrum) and speed-dependent angular anisotropy in the S- fragmentation. Our findings at the resonance of OCS at 6.5 eV closely align with the prediction of vibronic intensity borrowing by Orlandi and Siebrand [J. Chem. Phys. 58, 4513 (1973)].
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Affiliation(s)
- Narayan Kundu
- Department of Physical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur 741246, India
| | - Dhananjay Nandi
- Department of Physical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur 741246, India
- Center for Atomic, Molecular and Optical Sciences and Technologies, Joint Initiative of IIT Tirupati and IISER Tirupati, Yerpedu 517619, Andhra Pradesh, India
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3
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Verma P, Mukherjee M, Bhattacharya D, Haritan I, Dutta AK. Shape resonance induced electron attachment to cytosine: The effect of aqueous media. J Chem Phys 2023; 159:214303. [PMID: 38038205 DOI: 10.1063/5.0157576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 08/31/2023] [Indexed: 12/02/2023] Open
Abstract
We have investigated the impact of microsolvation on shape-type resonance states of nucleobases, taking cytosine as a case study. To characterize the resonance position and decay width of the metastable states, we employed the newly developed DLPNO-based EA-EOM-CCSD method in conjunction with the resonance via Padé (RVP) method. Our calculations show that the presence of water molecules causes a redshift in the resonance position and an increase in the lifetime for the three lowest-lying resonance states of cytosine. Furthermore, there are some indications that the lowest resonance state in isolated cytosine may get converted to a bound state in the presence of an aqueous environment. The obtained results are extremely sensitive to the basis set used for the calculations.
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Affiliation(s)
- Pooja Verma
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Madhubani Mukherjee
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482, USA
| | - Debarati Bhattacharya
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| | - Idan Haritan
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa 3200003, Israel
- Faculty of Engineering, Bar-Ilan University, Ramat Gan, Israel
| | - Achintya Kumar Dutta
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
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4
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Narayanan S J J, Tripathi D, Verma P, Adhikary A, Dutta AK. Secondary Electron Attachment-Induced Radiation Damage to Genetic Materials. ACS OMEGA 2023; 8:10669-10689. [PMID: 37008102 PMCID: PMC10061531 DOI: 10.1021/acsomega.2c06776] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Accepted: 02/20/2023] [Indexed: 06/19/2023]
Abstract
Reactions of radiation-produced secondary electrons (SEs) with biomacromolecules (e.g., DNA) are considered one of the primary causes of radiation-induced cell death. In this Review, we summarize the latest developments in the modeling of SE attachment-induced radiation damage. The initial attachment of electrons to genetic materials has traditionally been attributed to the temporary bound or resonance states. Recent studies have, however, indicated an alternative possibility with two steps. First, the dipole-bound states act as a doorway for electron capture. Subsequently, the electron gets transferred to the valence-bound state, in which the electron is localized on the nucleobase. The transfer from the dipole-bound to valence-bound state happens through a mixing of electronic and nuclear degrees of freedom. In the presence of aqueous media, the water-bound states act as the doorway state, which is similar to that of the presolvated electron. Electron transfer from the initial doorway state to the nucleobase-bound state in the presence of bulk aqueous media happens on an ultrafast time scale, and it can account for the decrease in DNA strand breaks in aqueous environments. Analyses of the theoretically obtained results along with experimental data have also been discussed.
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Affiliation(s)
- Jishnu Narayanan S J
- Department
of Chemistry, Indian Institute of Technology
Bombay, Powai, Mumbai 400076, India
| | - Divya Tripathi
- Department
of Chemistry, Indian Institute of Technology
Bombay, Powai, Mumbai 400076, India
| | - Pooja Verma
- Department
of Chemistry, Indian Institute of Technology
Bombay, Powai, Mumbai 400076, India
| | - Amitava Adhikary
- Department
of Chemistry, Oakland University, 146 Library Drive, Rochester, Michigan 48309, United States
| | - Achintya Kumar Dutta
- Department
of Chemistry, Indian Institute of Technology
Bombay, Powai, Mumbai 400076, India
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5
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Falkiewicz K, Kozak W, Zdrowowicz M, Spisz P, Chomicz-Mańka L, Torchala M, Rak J. Why 6-Iodouridine Cannot Be Used as a Radiosensitizer of DNA Damage? Computational and Experimental Studies. J Phys Chem B 2023; 127:2565-2574. [PMID: 36893332 PMCID: PMC10041638 DOI: 10.1021/acs.jpcb.3c00548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
Abstract
Previous density functional theory (DFT) studies on 6-brominated pyrimidine nucleosides suggest that 6-iodo-2'-deoxyuridine (6IdU) should act as a better radiosensitizer than its 5-iodosubstituted 2'-deoxyuridine analogue. In this work, we show that 6IdU is unstable in an aqueous solution. Indeed, a complete disappearance of the 6IdU signal was observed during its isolation by reversed-phase high-performance liquid chromatography (RP-HPLC). As indicated by the thermodynamic characteristics for the SN1-type hydrolysis of 6IdU obtained at the CAM-B3LYP/DGDZVP++ level and the polarizable continuum model (PCM) of water, 6-iodouracil (6IU) was already released quantitatively at ambient temperatures. The simulation of the hydrolysis kinetics demonstrated that a thermodynamic equilibrium was reached within seconds for the title compound. To assess the reliability of the calculations carried out, we synthesized 6-iodouridine (6IUrd), which was, unlike 6IdU, sufficiently stable in an aqueous solution at room temperature. The activation barrier for the N-glycosidic bond dissociation in 6IUrd was estimated experimentally using an Arrhenius plot. The stabilities in water calculated for 6IdU, 6IUrd, and 5-iodo-2'-deoxyuridine (5IdU) could be explained by the electronic and steric effects of the 2'-hydroxy group present in the ribose moiety. Our studies highlight the issue of the hydrolytic stability of potentially radiosensitizing nucleotides which, besides having favorable dissociative electron attachment (DEA) characteristics, must be stable in water to have any practical application.
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Affiliation(s)
- Karina Falkiewicz
- Laboratory of Biological Sensitizers, Department of Physical Chemistry, Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Witold Kozak
- Laboratory of Biological Sensitizers, Department of Physical Chemistry, Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Magdalena Zdrowowicz
- Laboratory of Biological Sensitizers, Department of Physical Chemistry, Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Paulina Spisz
- Laboratory of Biological Sensitizers, Department of Physical Chemistry, Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
- Laboratory of Intermolecular Interactions, Department of Bioinorganic Chemistry, Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Lidia Chomicz-Mańka
- Laboratory of Biological Sensitizers, Department of Physical Chemistry, Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Mieczyslaw Torchala
- Laboratory of Biological Sensitizers, Department of Physical Chemistry, Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Janusz Rak
- Laboratory of Biological Sensitizers, Department of Physical Chemistry, Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
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Narayanan S J J, Bachhar A, Tripathi D, Dutta AK. Electron Attachment to Wobble Base Pairs. J Phys Chem A 2023; 127:457-467. [PMID: 36622294 DOI: 10.1021/acs.jpca.2c07469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
We have analyzed the low-energy electron attachment to wobble base pairs using the equation of motion coupled cluster method and extended basis sets. A doorway mechanism exists for the attachment of the additional electron to the base pairs, where the initially formed dipole-bound anion captures the incoming electron. The doorway dipole-bound anionic state subsequently leads to the formation of a valence-bound state, and the transfer of extra electron occurs by mixing of electronic and nuclear degrees of freedom. The formation of the valence-bound anion is associated with proton transfer in hypoxanthine-cytosine and hypoxanthine-adenine base pairs, which happens through a concerted electron-proton transfer process. The calculated rate constant for the dipole-bound to valence-bound transition in wobble base pairs is slower than that observed in the Watson-Crick guanine-cytosine base pair.
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Affiliation(s)
- Jishnu Narayanan S J
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai400076, India
| | - Arnab Bachhar
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai400076, India
| | - Divya Tripathi
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai400076, India
| | - Achintya Kumar Dutta
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai400076, India
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7
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The role of repulsive and attractive forces in low-energy (3–15 eV) electron stimulated desorption of anions from molecular layers grown on clean and contaminated metallic substrates. Chem Phys 2023. [DOI: 10.1016/j.chemphys.2022.111661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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8
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Paul A, Nandi D. Dissociative electron attachment dynamics of carbon disulfide and violation of axial recoil approximation near 6 eV resonance. Phys Chem Chem Phys 2022; 24:21020-21029. [PMID: 36000546 DOI: 10.1039/d2cp02362h] [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
Complete dissociation dynamics of low-energy electron attachment to carbon disulfide have been studied using the velocity slice imaging (VSI) technique. The ion yields of the different fragment anions produced due to the dissociative electron attachment to carbon disulfide for the 5 to 11 eV incident electron energy range have been collected. Two resonances for S- ions are observed at around 6.2 eV and 7.7 eV, while only one resonance for both the CS- and S2- ions at 6.2 eV is present in this energy range. The kinetic energy and the angular distributions of these fragment negative ions at different incident electron energies around the 6.2 eV resonance have been extracted from the velocity slice images. These experimentally obtained angular distributions of different fragment anions combined with previous theoretical calculations provide a detailed picture of the breakdown of axial recoil approximation and the complete dissociation dynamics involved in this resonance.
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Affiliation(s)
- Anirban Paul
- Indian Institute of Science Education and Research Kolkata, Mohanpur 741246, India.
| | - Dhananjay Nandi
- Indian Institute of Science Education and Research Kolkata, Mohanpur 741246, India. .,Center for Atomic, Molecular and Optical Sciences & Technologies, Joint initiative of IIT Tirupati & IISER Tirupati, Yerpedu, 517619, Andhra Pradesh, India.
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9
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Kang DH, Kim J, Eun HJ, Kim SK. Experimental Observation of the Resonant Doorways to Anion Chemistry: Dynamic Role of Dipole-Bound Feshbach Resonances in Dissociative Electron Attachment. J Am Chem Soc 2022; 144:16077-16085. [PMID: 35973092 DOI: 10.1021/jacs.2c06334] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Anion chemical dynamics of autodetachment and fragmentation mediated by the dipole-bound state (DBS) have been thoroughly investigated in a state-specific way by employing the picosecond time-resolved or the nanosecond frequency-resolved spectroscopy combined with the cryogenically cooled ion trap and velocity-map imaging techniques. For the ortho-, meta-, or para-iodophenoxide anion (o-, m-, or p-IPhO-), the C-I bond rupture occurs via the nonadiabatic transition from the DBS to the nearby valence-bound states (VBS) of the anion where the vibronic coupling into the S1 (πσ*) state (repulsive along the C-I bond extension coordinate) should be largely responsible. Dynamic details are governed by the isomer-specific nature of the potential energy surfaces in the vicinity of the DBS-VBS curve crossings, as manifested in the huge different chemical reactivity of o-, m-, or p-IPhO-. It is confirmed here that the C-I bond dissociation is mediated by DBS resonances, providing the foremost evidence that the metastable DBS plays the critical role as the doorway into the anion chemistry especially of the dissociative electron attachment (DEA). The fragmentation channel is dominant when it is mediated by the DBS resonances located below the electron-affinity (EA) threshold, whereas it is kinetically adjusted by the competitive autodetachment when the DBS resonances above EA convey the electron to the valence orbitals. The product yield of the C-I bond cleavage is strongly mode-dependent as the rate of the concomitant autodetachment is much influenced by the characteristics of the individual vibrational modes, paving a new way of the reaction control of the anion chemistry.
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Affiliation(s)
- Do Hyung Kang
- Department of Chemistry, KAIST, Daejeon 34141, Republic of Korea
| | - Jinwoo Kim
- Department of Chemistry, KAIST, Daejeon 34141, Republic of Korea
| | - Han Jun Eun
- Department of Chemistry, KAIST, Daejeon 34141, Republic of Korea
| | - Sang Kyu Kim
- Department of Chemistry, KAIST, Daejeon 34141, Republic of Korea
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10
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Bouskila G, Landau A, Haritan I, Moiseyev N, Bhattacharya D. Complex energies and transition dipoles for shape-type resonances of uracil anion from stabilization curves via Padé. J Chem Phys 2022; 156:194101. [PMID: 35597649 DOI: 10.1063/5.0086887] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Absorption of slow moving electrons by neutral ground state nucleobases has been known to produce resonance metastable states. There are indications that such metastable states may play a key role in DNA/RNA damage. Therefore, herein, we present an ab initio non-Hermitian investigation of the resonance positions and decay rates for the low lying shape-type states of the uracil anion. In addition, we calculate the complex transition dipoles between these resonance states. We employ the resonance via Padé (RVP) method to calculate these complex properties from real stabilization curves by analytical dilation into the complex plane. This method has already been successfully applied to many small molecular systems, and herein, we present the first application of RVP to a medium-sized system. The presented resonance energies are optimized with respect to the size of the basis set and compared with previous theoretical studies and experimental findings. Complex transition dipoles between the shape-type resonances are computed using the optimal basis set. The ability to calculate ab initio energies and lifetimes of biologically relevant systems paves the way for studying reactions of such systems in which autoionization takes place, while the ability to also calculate their complex transition dipoles opens the door for studying photo-induced dynamics of such biological molecules.
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Affiliation(s)
- Gal Bouskila
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| | - Arie Landau
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| | - Idan Haritan
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| | - Nimrod Moiseyev
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| | - Debarati Bhattacharya
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa 3200003, Israel
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11
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Narayanan S J J, Tripathi D, Dutta AK. Doorway Mechanism for Electron Attachment Induced DNA Strand Breaks. J Phys Chem Lett 2021; 12:10380-10387. [PMID: 34669407 DOI: 10.1021/acs.jpclett.1c02735] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
We report a new doorway mechanism for the dissociative electron attachment to genetic materials. The dipole-bound state of the nucleotide anion acts as the doorway for electron capture in the genetic material. The electron gets subsequently transferred to a dissociative σ*-type anionic state localized on a sugar-phosphate or a sugar-nucleobase bond, leading to their cleavage. The electron transfer is mediated by the mixing of electronic and nuclear degrees of freedom. The cleavage rate of the sugar-phosphate bond predicted by this new mechanism is higher than that of the sugar-nucleobase bond breaking, and both processes are considerably slower than the formation of a stable valence-bound anion. The new mechanism can explain the relative rates of electron attachment induced bond cleavages in genetic materials.
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Affiliation(s)
- Jishnu Narayanan S J
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Divya Tripathi
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Achintya Kumar Dutta
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
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12
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Gao Y, Zheng Y, Sanche L. Low-Energy Electron Damage to Condensed-Phase DNA and Its Constituents. Int J Mol Sci 2021; 22:7879. [PMID: 34360644 PMCID: PMC8345953 DOI: 10.3390/ijms22157879] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 06/30/2021] [Accepted: 06/30/2021] [Indexed: 11/18/2022] Open
Abstract
The complex physical and chemical reactions between the large number of low-energy (0-30 eV) electrons (LEEs) released by high energy radiation interacting with genetic material can lead to the formation of various DNA lesions such as crosslinks, single strand breaks, base modifications, and cleavage, as well as double strand breaks and other cluster damages. When crosslinks and cluster damages cannot be repaired by the cell, they can cause genetic loss of information, mutations, apoptosis, and promote genomic instability. Through the efforts of many research groups in the past two decades, the study of the interaction between LEEs and DNA under different experimental conditions has unveiled some of the main mechanisms responsible for these damages. In the present review, we focus on experimental investigations in the condensed phase that range from fundamental DNA constituents to oligonucleotides, synthetic duplex DNA, and bacterial (i.e., plasmid) DNA. These targets were irradiated either with LEEs from a monoenergetic-electron or photoelectron source, as sub-monolayer, monolayer, or multilayer films and within clusters or water solutions. Each type of experiment is briefly described, and the observed DNA damages are reported, along with the proposed mechanisms. Defining the role of LEEs within the sequence of events leading to radiobiological lesions contributes to our understanding of the action of radiation on living organisms, over a wide range of initial radiation energies. Applications of the interaction of LEEs with DNA to radiotherapy are briefly summarized.
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Affiliation(s)
- Yingxia Gao
- State Key Laboratory of Photocatalysis on Energy and Environment, Fuzhou University, Fuzhou 350116, China;
| | - Yi Zheng
- State Key Laboratory of Photocatalysis on Energy and Environment, Fuzhou University, Fuzhou 350116, China;
| | - Léon Sanche
- Département de Médecine Nucléaire et Radiobiologie et Centre de Recherche Clinique, Faculté de Médecine, Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada;
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13
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Castellani ME, Verlet JRR. Intramolecular Photo-Oxidation as a Potential Source to Probe Biological Electron Damage: A Carboxylated Adenosine Analogue as Case Study. Molecules 2021; 26:2877. [PMID: 34067988 PMCID: PMC8152231 DOI: 10.3390/molecules26102877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 05/05/2021] [Accepted: 05/10/2021] [Indexed: 11/16/2022] Open
Abstract
A carboxylated adenosine analog (C-Ado-) has been synthesized and probed via time-resolved photoelectron spectroscopy in order to induce intra-molecular charge transfer from the carboxylic acid moiety to the nucleobase. Intra-molecular charge transfer can be exploited as starting point to probe low-energy electron (LEE) damage in DNA and its derivatives. Time-dependent density functional theory (TD-DFT) calculations at the B3LYP-6311G level of theory have been performed to verify that the highest occupied molecular orbital (HOMO) was located on carboxylic acid and that the lowest occupied molecular orbital (LUMO) was on the nucleobase. Hence, the carboxylic acid could work as electron source, whilst the nucleobase could serve the purpose of electron acceptor. The dynamics following excitation at 4.66 eV (266 nm) were probed using time-resolved photoelectron spectroscopy using probes at 1.55 eV (800 nm) and 3.10 eV (400 nm). The data show rapid decay of the excited state population and, based on the similarity of the overall dynamics to deoxy-adenosine monophosphate (dAMP-), it appears that the dominant decay mechanism is internal conversion following 1ππ* excitation of the nucleobase, rather than charge-transfer from the carboxylic acid to the nucleobase.
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14
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Dong Y, Liao H, Gao Y, Cloutier P, Zheng Y, Sanche L. Early Events in Radiobiology: Isolated and Cluster DNA Damage Induced by Initial Cations and Nonionizing Secondary Electrons. J Phys Chem Lett 2021; 12:717-723. [PMID: 33400538 DOI: 10.1021/acs.jpclett.0c03341] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Radiobiological damage is principally triggered by an initial cation and a secondary electron (SE). We address the fundamental questions: What lesions are first produced in DNA by this cation or nonionizing SE? What are their relative contributions to isolated and potentially lethal cluster lesions? Five monolayer films of dry plasmid DNA deposited on graphite or tantalum substrates are bombarded by 0.1-100 eV electrons in a vacuum. From measurements of the current transmitted through the films, 3.5 and 4.5 cations per incident 60 and 100 eV electrons, respectively, are estimated to be produced and stabilized within DNA. Damage analysis at 6, 10, 20, 30, 60, and 100 eV indicates that essentially all lesions, but preferentially cluster damages, are produced by non-ionizing or weakly ionizing electrons of energies below 12 eV. Most of these lesions are induced within femtosecond times, via transient anions and electron transfer within DNA, with little contributions from the numerous cations.
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Affiliation(s)
- Yanfang Dong
- State Key Laboratory of Photocatalysis on Energy and Environment, Fuzhou University, Fuzhou 350116, P.R. China
| | - Hong Liao
- State Key Laboratory of Photocatalysis on Energy and Environment, Fuzhou University, Fuzhou 350116, P.R. China
| | - Yingxia Gao
- State Key Laboratory of Photocatalysis on Energy and Environment, Fuzhou University, Fuzhou 350116, P.R. China
| | - Pierre Cloutier
- Department of Nuclear Medicine and Radiobiology and Clinical Research Center, Faculty of Medicine, Université de Sherbrooke, Sherbrooke, QC, Canada J1H 5N4
| | - Yi Zheng
- State Key Laboratory of Photocatalysis on Energy and Environment, Fuzhou University, Fuzhou 350116, P.R. China
| | - Léon Sanche
- Department of Nuclear Medicine and Radiobiology and Clinical Research Center, Faculty of Medicine, Université de Sherbrooke, Sherbrooke, QC, Canada J1H 5N4
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15
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Pshenichnyuk SA, Modelli A, Asfandiarov NL, Komolov AS. Ionizing radiation and natural constituents of living cells: Low-energy electron interaction with coenzyme Q analogs. J Chem Phys 2020; 153:111103. [PMID: 32962391 DOI: 10.1063/5.0022188] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Resonance electron attachment to short-tail analogs of coenzyme Q10 is investigated in the electron energy range 0 eV-14 eV under gas-phase conditions by means of dissociative electron attachment spectroscopy. Formation of long-lived (milliseconds) molecular negative ions is detected at 1.2 eV, but not at thermal energy. A huge increase in the electron detachment time as compared with the reference para-benzoquinone (40 µs) is ascribed to the presence of the isoprene side chains. Elimination of a neutral CH3 radical is found to be the most intense decay detected on the microsecond time scale. The results give some insight into the timescale of electron-driven processes stimulated in living tissues by high-energy radiation and are of importance in prospective fields of radiobiology and medicine.
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Affiliation(s)
- Stanislav A Pshenichnyuk
- Institute of Molecule and Crystal Physics, Ufa Federal Research Centre, Russian Academy of Sciences, Prospekt Oktyabrya 151, 450075 Ufa, Russia
| | - Alberto Modelli
- Università di Bologna, Dipartimento di Chimica "G. Ciamician", Via Selmi 2, 40126 Bologna, Italy
| | - Nail L Asfandiarov
- Institute of Molecule and Crystal Physics, Ufa Federal Research Centre, Russian Academy of Sciences, Prospekt Oktyabrya 151, 450075 Ufa, Russia
| | - Alexey S Komolov
- St. Petersburg State University, Universitetskaya nab. 7/9, 199034 St. Petersburg, Russia
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16
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Ali E, Chakraborty HS, Madison DH. Improved theoretical calculations for electron-impact ionization of DNA analogue molecules. J Chem Phys 2020; 152:124303. [PMID: 32241131 DOI: 10.1063/1.5143148] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Ionizing interactions between charged particles and molecules of biological relevance have attracted considerable interest in the last decade due to its importance in medical radiation therapy. We have previously calculated triply differential cross sections for five biomolecules in collaboration with experimental groups. We used the molecular 3-body distorted wave approximation for these calculations. For ionization of biomolecules, experimentalists are unable to determine the orientation of the molecule at the time of ionization, which means that the calculated cross sections need to be averaged over all molecular orientations. At the time the calculations were performed, it was not numerically feasible for us to perform proper averaging over orientations, so we introduced the orientation averaged molecular orbital approximation to make the calculations possible. We now have the computational capability to properly perform this average, so, here, we present new results with a proper average over orientations and compare with the previous calculations and experiment. Since the original calculations, results from two different distorted-wave models have also been published and the new results will also be compared with those calculations. Overall, the new results are in better agreement with the experiment.
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Affiliation(s)
- Esam Ali
- Department of Natural Sciences, D. L. Hubbard Center for Innovation, Northwest Missouri State University, Maryville, Missouri 64468, USA
| | - H S Chakraborty
- Department of Natural Sciences, D. L. Hubbard Center for Innovation, Northwest Missouri State University, Maryville, Missouri 64468, USA
| | - D H Madison
- Missouri University of Science and Technology, Rolla, Missouri 65402, USA
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17
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Alvarez-Ibarra A, Parise A, Hasnaoui K, de la Lande A. The physical stage of radiolysis of solvated DNA by high-energy-transfer particles: insights from new first principles simulations. Phys Chem Chem Phys 2020; 22:7747-7758. [DOI: 10.1039/d0cp00165a] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Electron dynamics simulations based on density functional theory are carried out on nanometric molecular systems to decipher the primary processes following irradiation of bio-macromolecules by high energy transfer charged particles.
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Affiliation(s)
| | - Angela Parise
- Université Paris-Saclay
- CNRS
- Institut de Chimie Physique UMR8000
- Orsay
- France
| | - Karim Hasnaoui
- Institut du Développement et des Ressources en Informatique Scientifique
- Rue John von Neumann
- Orsay
- France
- Maison de la Simulation
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18
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Chakraborty D, Giri A, Nandi D. Dissociation dynamics in low energy electron attachment to ammonia using velocity slice imaging. Phys Chem Chem Phys 2019; 21:21908-21917. [PMID: 31553032 DOI: 10.1039/c9cp03973b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The complete dissociation dynamics of low energy electron attachment to the ammonia molecule has been studied using velocity slice imaging (VSI) spectrometry. One low energy resonant peak around 5.5 eV and a broad resonance around 10.5 eV incident electron energies have been observed. The resonant states mainly dissociate via H- and NH2- fragments, though for the upper resonant state, the signature of NH- fragments is also predicted due to a three-body dissociation process. Kinetic energy and angular distributions of the NH2- fragment anions are measured simultaneously around the two resonances. Based on our experimental observations, we conclude that a temporary negative ion (TNI) state with A1 symmetry is responsible for the lower resonance. Whereas, we find strong evidence for the existence of a TNI state having A1 symmetry at the 10.5 eV resonance for the first time.
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Affiliation(s)
- Dipayan Chakraborty
- Indian Institute of Science Education and Research Kolkata, Mohanpur 741246, India.
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19
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Giacomozzi L, D’Angelo G, Diaz-Tendero S, de Ruette N, Stockett MH, Alcamí M, Cederquist H, Schmidt HT, Zettergren H. Decay pathways for protonated and deprotonated adenine molecules. J Chem Phys 2019; 151:044306. [DOI: 10.1063/1.5109963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- L. Giacomozzi
- Department of Physics, Stockholm University, Stockholm SE-106 91, Sweden
| | - G. D’Angelo
- Department of Physics, Stockholm University, Stockholm SE-106 91, Sweden
- Departamento de Química, Módulo 13, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - S. Diaz-Tendero
- Departamento de Química, Módulo 13, Universidad Autónoma de Madrid, 28049 Madrid, Spain
- Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, 28049 Madrid, Spain
- Institute for Advanced Research in Chemical Sciences (IAdChem), Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - N. de Ruette
- Department of Physics, Stockholm University, Stockholm SE-106 91, Sweden
| | - M. H. Stockett
- Department of Physics, Stockholm University, Stockholm SE-106 91, Sweden
| | - M. Alcamí
- Departamento de Química, Módulo 13, Universidad Autónoma de Madrid, 28049 Madrid, Spain
- Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, 28049 Madrid, Spain
- Institute for Advanced Research in Chemical Sciences (IAdChem), Universidad Autónoma de Madrid, 28049 Madrid, Spain
- Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA-NANO), 28049 Madrid, Spain
| | - H. Cederquist
- Department of Physics, Stockholm University, Stockholm SE-106 91, Sweden
| | - H. T. Schmidt
- Department of Physics, Stockholm University, Stockholm SE-106 91, Sweden
| | - H. Zettergren
- Department of Physics, Stockholm University, Stockholm SE-106 91, Sweden
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20
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Dong Y, Gao Y, Liu W, Gao T, Zheng Y, Sanche L. Clustered DNA Damage Induced by 2-20 eV Electrons and Transient Anions: General Mechanism and Correlation to Cell Death. J Phys Chem Lett 2019; 10:2985-2990. [PMID: 31099579 DOI: 10.1021/acs.jpclett.9b01063] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The mechanisms of action of low-energy electrons (LEEs) generated in large quantities by ionizing radiation constitute an essential element of our understanding of early events in radiolysis and radiobiology. We present the 2-20 eV electron energy dependence of the yields of base damage (BD), BD-related cross-links (CLs), and non-double-strand break (NDSB) clustered damage induced in DNA. These new yield functions are generated by the impact of LEEs on plasmid DNA films. The damage is analyzed by gel electrophoresis with and without enzyme treatment. Maxima at 5 and 10 eV in BDs and BD-related CLs yield functions, and two others, at 6 and 10 eV, in those of NDSB clustered damage are ascribed to core-excited transient anions that decay into bond-breaking channels. The mechanism causing all types of DNA damages can be attributed to the capture of a single electron by a base followed by multiple different electron transfer pathways.
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Affiliation(s)
- Yanfang Dong
- State Key Laboratory of Photocatalysis on Energy and Environment, Faculty of Chemistry , Fuzhou University , Fuzhou 350116 , P. R. China
| | - Yingxia Gao
- State Key Laboratory of Photocatalysis on Energy and Environment, Faculty of Chemistry , Fuzhou University , Fuzhou 350116 , P. R. China
| | - Wenhui Liu
- State Key Laboratory of Photocatalysis on Energy and Environment, Faculty of Chemistry , Fuzhou University , Fuzhou 350116 , P. R. China
| | - Ting Gao
- State Key Laboratory of Photocatalysis on Energy and Environment, Faculty of Chemistry , Fuzhou University , Fuzhou 350116 , P. R. China
| | - Yi Zheng
- State Key Laboratory of Photocatalysis on Energy and Environment, Faculty of Chemistry , Fuzhou University , Fuzhou 350116 , P. R. China
| | - Léon Sanche
- Department of Nuclear Medicine and Radiobiology and Clinical Research Center, Faculty of Medicine , Université de Sherbrooke , Sherbrooke , QC , Canada J1H 5N4
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21
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Vogel S, Ebel K, Schürmann RM, Heck C, Meiling T, Milosavljevic AR, Giuliani A, Bald I. Vacuum-UV and Low-Energy Electron-Induced DNA Strand Breaks - Influence of the DNA Sequence and Substrate. Chemphyschem 2019; 20:823-830. [PMID: 30719805 DOI: 10.1002/cphc.201801152] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 02/01/2019] [Indexed: 12/28/2022]
Abstract
DNA is effectively damaged by radiation, which can on the one hand lead to cancer and is on the other hand directly exploited in the treatment of tumor tissue. DNA strand breaks are already induced by photons having an energy below the ionization energy of DNA. At high photon energies, most of the DNA strand breaks are induced by low-energy secondary electrons. In the present study we quantified photon and electron induced DNA strand breaks in four different 12mer oligonucleotides. They are irradiated directly with 8.44 eV vacuum ultraviolet (VUV) photons and 8.8 eV low energy electrons (LEE). By using Si instead of VUV transparent CaF2 as a substrate the VUV exposure leads to an additional release of LEEs, which have a maximum energy of 3.6 eV and can significantly enhance strand break cross sections. Atomic force microscopy is used to visualize strand breaks on DNA origami platforms and to determine absolute values for the strand break cross sections. Upon irradiation with 8.44 eV photons all the investigated sequences show very similar strand break cross sections in the range of 1.7-2.3×10-16 cm2 . The strand break cross sections for LEE irradiation at 8.8 eV are one to two orders of magnitude larger than the ones for VUV photons, and a slight sequence dependence is observed. The sequence dependence is even more pronounced for LEEs with energies <3.6 eV. The present results help to assess DNA damage by photons and electrons close to the ionization threshold.
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Affiliation(s)
- Stefanie Vogel
- Institute of Chemistry - Physical Chemistry, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476, Potsdam, Germany.,Department 1 - Analytical Chemistry and Reference Materials, BAM Federal Institute of Materials Research and Testing, Richard-Willstätter Str. 11, 12489, Berlin, Germany.,School of Analytical Sciences Adlershof, Humboldt-Universität zu Berlin, Unter den Linden 6, 10099, Germany
| | - Kenny Ebel
- Institute of Chemistry - Physical Chemistry, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476, Potsdam, Germany.,Department 1 - Analytical Chemistry and Reference Materials, BAM Federal Institute of Materials Research and Testing, Richard-Willstätter Str. 11, 12489, Berlin, Germany
| | - Robin M Schürmann
- Department 1 - Analytical Chemistry and Reference Materials, BAM Federal Institute of Materials Research and Testing, Richard-Willstätter Str. 11, 12489, Berlin, Germany
| | - Christian Heck
- Institute of Chemistry - Physical Chemistry, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476, Potsdam, Germany.,Department 1 - Analytical Chemistry and Reference Materials, BAM Federal Institute of Materials Research and Testing, Richard-Willstätter Str. 11, 12489, Berlin, Germany.,School of Analytical Sciences Adlershof, Humboldt-Universität zu Berlin, Unter den Linden 6, 10099, Germany
| | - Till Meiling
- Institute of Chemistry - Physical Chemistry, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476, Potsdam, Germany
| | | | - Alexandre Giuliani
- Synchrotron SOLEIL, 91192, Gif-sur-Yvette, France.,UAR 1008 CEPIA, INRA, 44316, Nantes, France
| | - Ilko Bald
- Institute of Chemistry - Physical Chemistry, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476, Potsdam, Germany.,Department 1 - Analytical Chemistry and Reference Materials, BAM Federal Institute of Materials Research and Testing, Richard-Willstätter Str. 11, 12489, Berlin, Germany
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22
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Schmidt F, Swiderek P, Bredehöft JH. Electron-Induced Formation of Ethyl Methyl Ether in Condensed Mixtures of Methanol and Ethylene. J Phys Chem A 2018; 123:37-47. [DOI: 10.1021/acs.jpca.8b10209] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Fabian Schmidt
- University of Bremen, Institute of Applied and Physical Chemistry, Fachbereich 2 (Chemie/Biologie), Leobener Straße/NW 2, Postfach 330440, D-28334 Bremen, Germany
| | - Petra Swiderek
- University of Bremen, Institute of Applied and Physical Chemistry, Fachbereich 2 (Chemie/Biologie), Leobener Straße/NW 2, Postfach 330440, D-28334 Bremen, Germany
| | - Jan H. Bredehöft
- University of Bremen, Institute of Applied and Physical Chemistry, Fachbereich 2 (Chemie/Biologie), Leobener Straße/NW 2, Postfach 330440, D-28334 Bremen, Germany
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23
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Szczerbiński J, Gyr L, Kaeslin J, Zenobi R. Plasmon-Driven Photocatalysis Leads to Products Known from E-beam and X-ray-Induced Surface Chemistry. NANO LETTERS 2018; 18:6740-6749. [PMID: 30277787 DOI: 10.1021/acs.nanolett.8b02426] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Plasmonic metal nanostructures can concentrate incident optical fields in nanometer-sized volumes, called hot spots. This leads to enhanced optical responses of molecules in such a hot spot but also to chemical transformations, driven by plasmon-induced hot carriers. Here, we employ tip-enhanced Raman spectroscopy (TERS) to study the mechanism of these reactions in situ at the level of a single hot spot. Direct spectroscopic measurements reveal the energy distribution of hot electrons, as well as the temperature changes due to plasmonic heating. Therefore, charge-driven reactions can be distinguished from thermal reaction pathways. The products of the hot-carrier-driven reactions are strikingly similar to the ones known from X-ray or e-beam-induced surface chemistry despite the >100-fold energy difference between visible and X-ray photons. Understanding the analogies between those two scenarios implies new strategies for rational design of plasmonic photocatalytic reactions and for the elimination of photoinduced damage in plasmon-enhanced spectroscopy.
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Affiliation(s)
- Jacek Szczerbiński
- Department of Chemistry and Applied Biosciences, Laboratory of Organic Chemistry , ETH Zurich , 8093 Zurich , Switzerland
| | - Luzia Gyr
- Department of Chemistry and Applied Biosciences, Laboratory of Organic Chemistry , ETH Zurich , 8093 Zurich , Switzerland
| | - Jérôme Kaeslin
- Department of Chemistry and Applied Biosciences, Laboratory of Organic Chemistry , ETH Zurich , 8093 Zurich , Switzerland
| | - Renato Zenobi
- Department of Chemistry and Applied Biosciences, Laboratory of Organic Chemistry , ETH Zurich , 8093 Zurich , Switzerland
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24
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Xu X, Gong M, Li X, Zhang SB, Chen X. Theoretical study of (e, 2e) triple differential cross sections of tetrahydrofuran using multicenter distorted-wave method. J Chem Phys 2018; 148:244104. [PMID: 29960345 DOI: 10.1063/1.5029428] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We present in this work a theoretical study of the triple differential cross sections for electron-impact single ionization of 12a' and 9b orbitals of a tetrahydrofuran molecule. The calculations are performed by the multicenter distorted-wave (MCDW) method in coplanar asymmetric kinematics with an incident electron energy of 250 eV, where previous (e, 2e) experiments and theories are available for comparison. The present calculations reproduce the experimental measurements satisfactorily, indicating that the MCDW method can be easily extended to study biomolecules with sufficiently high calculation efficiency.
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Affiliation(s)
- Xiaojie Xu
- Hefei National Laboratory for Physical Sciences at Microscale and Department of Modern Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Maomao Gong
- Hefei National Laboratory for Physical Sciences at Microscale and Department of Modern Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Xingyu Li
- Hefei National Laboratory for Physical Sciences at Microscale and Department of Modern Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Song Bin Zhang
- School of Physics and Information Technology, Shaanxi Normal University, Xian 710119, China
| | - Xiangjun Chen
- Hefei National Laboratory for Physical Sciences at Microscale and Department of Modern Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
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25
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Debiossac M, Schätti J, Kriegleder M, Geyer P, Shayeghi A, Mayor M, Arndt M, Köhler V. Tailored photocleavable peptides: fragmentation and neutralization pathways in high vacuum. Phys Chem Chem Phys 2018; 20:11412-11417. [PMID: 29645042 PMCID: PMC5932999 DOI: 10.1039/c8cp01058g] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 03/23/2018] [Indexed: 01/31/2023]
Abstract
Photocleavable tags (PCTs) have the potential for excellent spatio-temporal control over the release of subunits of complex molecules. Here, we show that electrosprayed oligopeptides, functionalized by a tailored ortho-nitroarylether can undergo site-specific photo-activated cleavage under UV irradiation (266 nm) in high vacuum. The comparison of UV photodissociation (UVPD) and collision-induced dissociation (CID) points to the thermal nature of the cleavage mechanism, a picture corroborated by the temperature dependence of the process. Two competing photodissociation pathways can be identified. In one case a phenolate anion is separated from a neutral zwitterion. In the other case a neutral phenol derivative leaves a negatively charged peptide behind. To understand the factors favoring one channel over the other, we investigate the influence of the peptide length, the nature of the phenolic group and the position of the nitro-group (ortho vs. para). The observed gas phase cleavage of a para-nitro benzylic ether markedly differs from the established behavior in solution.
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Affiliation(s)
- M. Debiossac
- Faculty of Physics, University of Vienna , VCQ, Boltzmanngasse 5 , A-1090 Vienna , Austria .
| | - J. Schätti
- Department of Chemistry, University of Basel , Mattenstrasse 24a, BPR 1096 , CH-4058 Basel , Switzerland .
| | - M. Kriegleder
- Faculty of Physics, University of Vienna , VCQ, Boltzmanngasse 5 , A-1090 Vienna , Austria .
| | - P. Geyer
- Faculty of Physics, University of Vienna , VCQ, Boltzmanngasse 5 , A-1090 Vienna , Austria .
| | - A. Shayeghi
- Faculty of Physics, University of Vienna , VCQ, Boltzmanngasse 5 , A-1090 Vienna , Austria .
| | - M. Mayor
- Department of Chemistry, University of Basel , Mattenstrasse 24a, BPR 1096 , CH-4058 Basel , Switzerland .
- Institute of Nanotechnology (INT), Karlsruhe Institute of Technology (KIT) , Hermann-von-Helmholtz-Platz 1 , D-76344 Eggenstein-Leopoldshafen , Germany
- Lehn Institute of Functional Materials (LIFM), Sun Yat-Sen University (SYSU) , Xingang Rd. W. , Guangzhou , China
| | - M. Arndt
- Faculty of Physics, University of Vienna , VCQ, Boltzmanngasse 5 , A-1090 Vienna , Austria .
| | - V. Köhler
- Department of Chemistry, University of Basel , Mattenstrasse 24a, BPR 1096 , CH-4058 Basel , Switzerland .
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26
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Kuncic Z, Lacombe S. Nanoparticle radio-enhancement: principles, progress and application to cancer treatment. Phys Med Biol 2018; 63:02TR01. [PMID: 29125831 DOI: 10.1088/1361-6560/aa99ce] [Citation(s) in RCA: 134] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Enhancement of radiation effects by high-atomic number nanoparticles (NPs) has been increasingly studied for its potential to improve radiotherapeutic efficacy. The underlying principle of NP radio-enhancement is the potential to release copious electrons into a nanoscale volume, thereby amplifying radiation-induced biological damage. While the vast majority of studies to date have focused on gold nanoparticles with photon radiation, an increasing number of experimental, theoretical and simulation studies have explored opportunities offered by other NPs (e.g. gadolinium, platinum, iron oxide, hafnium) and other therapeutic radiation sources such as ion beams. It is thus of interest to the research community to consolidate findings from the different studies and summarise progress to date, as well as to identify strategies that offer promising opportunities for clinical translation. This is the purpose of this Topical Review.
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Affiliation(s)
- Zdenka Kuncic
- School of Physics and Sydney Nano Institute, University of Sydney, Sydney, NSW 2006, Australia
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27
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Auger electron emission initiated by the creation of valence-band holes in graphene by positron annihilation. Nat Commun 2017; 8:16116. [PMID: 28703225 PMCID: PMC5511367 DOI: 10.1038/ncomms16116] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 05/31/2017] [Indexed: 11/08/2022] Open
Abstract
Auger processes involving the filling of holes in the valence band are thought to make important contributions to the low-energy photoelectron and secondary electron spectrum from many solids. However, measurements of the energy spectrum and the efficiency with which electrons are emitted in this process remain elusive due to a large unrelated background resulting from primary beam-induced secondary electrons. Here, we report the direct measurement of the energy spectra of electrons emitted from single layer graphene as a result of the decay of deep holes in the valence band. These measurements were made possible by eliminating competing backgrounds by employing low-energy positrons (<1.25 eV) to create valence-band holes by annihilation. Our experimental results, supported by theoretical calculations, indicate that between 80 and 100% of the deep valence-band holes in graphene are filled via an Auger transition. Auger processes are at the core of electron emission in solid-state physics, however measuring the spectra of electrons emitted solely as a result of Auger transitions remains a challenge. Here, the authors measure the electron energy spectrum in graphene and observe the prominence of Auger-like processes in its valence band.
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28
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Hahn MB, Meyer S, Kunte HJ, Solomun T, Sturm H. Measurements and simulations of microscopic damage to DNA in water by 30 keV electrons: A general approach applicable to other radiation sources and biological targets. Phys Rev E 2017; 95:052419. [PMID: 28618479 DOI: 10.1103/physreve.95.052419] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Indexed: 12/28/2022]
Abstract
The determination of the microscopic dose-damage relationship for DNA in an aqueous environment is of a fundamental interest for dosimetry and applications in radiation therapy and protection. We combine geant4 particle-scattering simulations in water with calculations concerning the movement of biomolecules to obtain the energy deposit in the biologically relevant nanoscopic volume. We juxtaposition these results to the experimentally determined damage to obtain the dose-damage relationship at a molecular level. This approach is tested for an experimentally challenging system concerning the direct irradiation of plasmid DNA (pUC19) in water with electrons as primary particles. Here a microscopic target model for the plasmid DNA based on the relation of lineal energy and radiation quality is used to calculate the effective target volume. It was found that on average fewer than two ionizations within a 7.5-nm radius around the sugar-phosphate backbone are sufficient to cause a single strand break, with a corresponding median lethal energy deposit being E_{1/2}=6±4 eV. The presented method is applicable for ionizing radiation (e.g., γ rays, x rays, and electrons) and a variety of targets, such as DNA, proteins, or cells.
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Affiliation(s)
- Marc Benjamin Hahn
- Institut für Experimentalphysik, Freie Universität Berlin, D-14195 Berlin, Germany and Bundesanstalt für Materialforschung und Prüfung, D-12205 Berlin, Germany
| | - Susann Meyer
- Institute of Biochemistry and Biology, University of Potsdam, D-14476 Potsdam, Germany and Bundesanstalt für Materialforschung und Prüfung, D-12205 Berlin, 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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29
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Verkhovtsev A, Traore A, Muñoz A, Blanco F, García G. Modeling secondary particle tracks generated by intermediate- and low-energy protons in water with the Low-Energy Particle Track Simulation code. Radiat Phys Chem Oxf Engl 1993 2017. [DOI: 10.1016/j.radphyschem.2016.09.021] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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30
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Haume K, Rosa S, Grellet S, Śmiałek MA, Butterworth KT, Solov’yov AV, Prise KM, Golding J, Mason NJ. Gold nanoparticles for cancer radiotherapy: a review. Cancer Nanotechnol 2016; 7:8. [PMID: 27867425 PMCID: PMC5095165 DOI: 10.1186/s12645-016-0021-x] [Citation(s) in RCA: 250] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 10/14/2016] [Indexed: 12/11/2022] Open
Abstract
Radiotherapy is currently used in around 50% of cancer treatments and relies on the deposition of energy directly into tumour tissue. Although it is generally effective, some of the deposited energy can adversely affect healthy tissue outside the tumour volume, especially in the case of photon radiation (gamma and X-rays). Improved radiotherapy outcomes can be achieved by employing ion beams due to the characteristic energy deposition curve which culminates in a localised, high radiation dose (in form of a Bragg peak). In addition to ion radiotherapy, novel sensitisers, such as nanoparticles, have shown to locally increase the damaging effect of both photon and ion radiation, when both are applied to the tumour area. Amongst the available nanoparticle systems, gold nanoparticles have become particularly popular due to several advantages: biocompatibility, well-established methods for synthesis in a wide range of sizes, and the possibility of coating of their surface with a large number of different molecules to provide partial control of, for example, surface charge or interaction with serum proteins. This gives a full range of options for design parameter combinations, in which the optimal choice is not always clear, partially due to a lack of understanding of many processes that take place upon irradiation of such complicated systems. In this review, we summarise the mechanisms of action of radiation therapy with photons and ions in the presence and absence of nanoparticles, as well as the influence of some of the core and coating design parameters of nanoparticles on their radiosensitisation capabilities.
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Affiliation(s)
- Kaspar Haume
- Department of Physical Sciences, The Open University, Walton Hall, Milton Keynes, MK7 6AA UK
| | - Soraia Rosa
- School of Medicine, Dentistry and Biomedical Sciences, Queen’s University Belfast, Lisburn Road, Belfast, BT9 7BL UK
| | - Sophie Grellet
- Department of Life, Health and Chemical Sciences, The Open University, Walton Hall, Milton Keynes, MK7 6AA UK
| | - Małgorzata A. Śmiałek
- Department of Control and Power Engineering, Faculty of Ocean Engineering and Ship Technology, Gdansk University of Technology, 80-233 Gdansk, Poland
| | - Karl T. Butterworth
- School of Medicine, Dentistry and Biomedical Sciences, Queen’s University Belfast, Lisburn Road, Belfast, BT9 7BL UK
| | | | - Kevin M. Prise
- School of Medicine, Dentistry and Biomedical Sciences, Queen’s University Belfast, Lisburn Road, Belfast, BT9 7BL UK
| | - Jon Golding
- Department of Life, Health and Chemical Sciences, The Open University, Walton Hall, Milton Keynes, MK7 6AA UK
| | - Nigel J. Mason
- Department of Physical Sciences, The Open University, Walton Hall, Milton Keynes, MK7 6AA UK
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Barbosa AS, Varella MTDN, Sanchez SD, Ameixa J, Blanco F, García G, Limão-Vieira P, Ferreira da Silva F, Bettega MHF. Theoretical and experimental study on electron interactions with chlorobenzene: Shape resonances and differential cross sections. J Chem Phys 2016; 145:084311. [DOI: 10.1063/1.4961649] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Alessandra Souza Barbosa
- Departamento de Física, Universidade Federal do Paraná, CP 19044, 81531-990 Curitiba, Paraná, Brazil
- Laboratório de Colisões Atómicas e Moleculares, CEFITEC, Departamento de Física, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Márcio T. do N. Varella
- Instituto de Física, Universidade de São Paulo, Rua do Matão 1731, 05508-090 São Paulo, SP, Brazil
| | - Sergio d’A. Sanchez
- Departamento de Física, Universidade Federal do Paraná, CP 19044, 81531-990 Curitiba, Paraná, Brazil
| | - João Ameixa
- Laboratório de Colisões Atómicas e Moleculares, CEFITEC, Departamento de Física, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Francisco Blanco
- Departamento de Física Atómica, Molecular y Nuclear, Facultad de Ciencias Físicas, Universidad Complutense de Madrid, E-28040 Madrid, Spain
| | - Gustavo García
- Instituto de Física Fundamental, Consejo Superior de Investigaciones Científicas (CSIC), Serrano 113-bis, 28006 Madrid, Spain
| | - Paulo Limão-Vieira
- Laboratório de Colisões Atómicas e Moleculares, CEFITEC, Departamento de Física, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Filipe Ferreira da Silva
- Laboratório de Colisões Atómicas e Moleculares, CEFITEC, Departamento de Física, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Márcio H. F. Bettega
- Departamento de Física, Universidade Federal do Paraná, CP 19044, 81531-990 Curitiba, Paraná, Brazil
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Stephansen AB, King SB, Yokoi Y, Minoshima Y, Li WL, Kunin A, Takayanagi T, Neumark DM. Dynamics of dipole- and valence bound anions in iodide-adenine binary complexes: A time-resolved photoelectron imaging and quantum mechanical investigation. J Chem Phys 2016; 143:104308. [PMID: 26374036 DOI: 10.1063/1.4929995] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Dipole bound (DB) and valence bound (VB) anions of binary iodide-adenine complexes have been studied using one-color and time-resolved photoelectron imaging at excitation energies near the vertical detachment energy. The experiments are complemented by quantum chemical calculations. One-color spectra show evidence for two adenine tautomers, the canonical, biologically relevant A9 tautomer and the A3 tautomer. In the UV-pump/IR-probe time-resolved experiments, transient adenine anions can be formed by electron transfer from the iodide. These experiments show signals from both DB and VB states of adenine anions formed on femto- and picosecond time scales, respectively. Analysis of the spectra and comparison with calculations suggest that while both the A9 and A3 tautomers contribute to the DB signal, only the DB state of the A3 tautomer undergoes a transition to the VB anion. The VB anion of A9 is higher in energy than both the DB anion and the neutral, and the VB anion is therefore not accessible through the DB state. Experimental evidence of the metastable A9 VB anion is instead observed as a shape resonance in the one-color photoelectron spectra, as a result of UV absorption by A9 and subsequent electron transfer from iodide into the empty π-orbital. In contrast, the iodide-A3 complex constitutes an excellent example of how DB states can act as doorway state for VB anion formation when the VB state is energetically available.
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Affiliation(s)
- Anne B Stephansen
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 København Ø, Denmark
| | - Sarah B King
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Yuki Yokoi
- Department of Chemistry, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama City, Saitama 338-8570, Japan
| | - Yusuke Minoshima
- Department of Chemistry, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama City, Saitama 338-8570, Japan
| | - Wei-Li Li
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Alice Kunin
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Toshiyuki Takayanagi
- Department of Chemistry, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama City, Saitama 338-8570, Japan
| | - Daniel M Neumark
- Department of Chemistry, University of California, Berkeley, California 94720, USA
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Dharmadhikari JA, Dharmadhikari AK, Kasuba KC, Bharambe H, D'Souza JS, Rathod KD, Mathur D. Optical control of filamentation-induced damage to DNA by intense, ultrashort, near-infrared laser pulses. Sci Rep 2016; 6:27515. [PMID: 27279565 PMCID: PMC4899723 DOI: 10.1038/srep27515] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 05/20/2016] [Indexed: 11/09/2022] Open
Abstract
We report on damage to DNA in an aqueous medium induced by ultrashort pulses of intense laser light of 800 nm wavelength. Focusing of such pulses, using lenses of various focal lengths, induces plasma formation within the aqueous medium. Such plasma can have a spatial extent that is far in excess of the Rayleigh range. In the case of water, the resulting ionization and dissociation gives rise to in situ generation of low-energy electrons and OH-radicals. Interactions of these with plasmid DNA produce nicks in the DNA backbone: single strand breaks (SSBs) are induced as are, at higher laser intensities, double strand breaks (DSBs). Under physiological conditions, the latter are not readily amenable to repair. Systematic quantification of SSBs and DSBs at different values of incident laser energy and under different external focusing conditions reveals that damage occurs in two distinct regimes. Numerical aperture is the experimental handle that delineates the two regimes, permitting simple optical control over the extent of DNA damage.
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Affiliation(s)
- J A Dharmadhikari
- Centre for Atomic and Molecular Physics, Manipal University, Manipal 576 104, India
| | - A K Dharmadhikari
- Tata Institute of Fundamental Research, 1 Homi Bhabha Road, Mumbai 400 005, India
| | - K C Kasuba
- UM-DAE Centre for Excellence in Basic Sciences, Kalina Campus, Santacruz (East), Mumbai 400 098, India
| | - H Bharambe
- UM-DAE Centre for Excellence in Basic Sciences, Kalina Campus, Santacruz (East), Mumbai 400 098, India
| | - J S D'Souza
- UM-DAE Centre for Excellence in Basic Sciences, Kalina Campus, Santacruz (East), Mumbai 400 098, India
| | - K D Rathod
- Tata Institute of Fundamental Research, 1 Homi Bhabha Road, Mumbai 400 005, India
| | - D Mathur
- Tata Institute of Fundamental Research, 1 Homi Bhabha Road, Mumbai 400 005, India
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Fong CW. Platinum anti-cancer drugs: Free radical mechanism of Pt-DNA adduct formation and anti-neoplastic effect. Free Radic Biol Med 2016; 95:216-29. [PMID: 27012421 DOI: 10.1016/j.freeradbiomed.2016.03.006] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2015] [Revised: 03/10/2016] [Accepted: 03/19/2016] [Indexed: 11/29/2022]
Abstract
The literature on the anti-neoplastic effects of Pt drugs provides substantial evidence that free radical may be involved in the formation of Pt-DNA adducts and other cytotoxic effects. The conditions specific to cancerous tumours are more conducive to free radical mechanisms than the commonly accepted hydrolysis nucleophilic-electrophilic mechanism of Pt-DNA adduct formation. Molecular orbital studies of the adiabatic attachment of hydrated electrons to Pt drugs reveal that there is a significant lengthening of the Pt-X bond (where X is Cl, O in cisplatin, carboplatin and some pyrophosphate-Pt drugs but not oxaliplatin) in the anion radical species. This observation is consistent with a dissociative electron transfer (DET) mechanism for the formation of Pt-DNA adducts. A DET reaction mechanism is proposed for the reaction of Pt drugs with guanine which involves a quasi-inner sphere 2 electron transfer process involving a transient intermediate 5 co-ordinated activated anion radical species {R2Pt---Cl(G)(Cl)•}*(-) (where R is an ammine group, and G is guanine) and the complex has an elongated Pt---Cl (or Pt---O) bond. A DET mechanism is also proposed when Pt drugs are activated by reaction with free radicals such as HO•, CO3•(-), O2•(-) but do not react with DNA bases to form adducts, but form Pt-protein adducts with proteins such ezrin, FAS, DR5, TNFR1 etc. The DET mechanism may not occur with oxaliplatin.
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35
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Gu J, Wang J, Leszczynski J. Electron interaction with a DNA duplex: dCpdC:dGpdG. Phys Chem Chem Phys 2016; 18:13657-65. [PMID: 27139598 DOI: 10.1039/c6cp01408a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Electron attachment to double-stranded cytosine-rich DNA, dCpdC:dGpdG, has been studied by density functional theory. This system represents a minimal descriptive unit of a cytosine-rich double-stranded DNA helix. A significant electron affinity for the formation of a cytosine-centered radical anion is revealed to be about 2.2 eV. The excess electron may reside on the nucleobase at the 5' position (dC˙(-)pdC:dGpdG) or at the 3' position (dCpdC˙(-):dGpdG). The inter-strand proton transfer between the radical anion centered cytosine (N3) and the paired guanine (HN1) results in the formation of radical anion center separated complexes dC1H˙pdC:dG2-H(-)pdG and dCpdC2H˙:dGpdG1-H(-). These distonic radical anions are found to be approximately 1 to 4 kcal mol(-1) more stable than the normal radical anions. Intra-strand cytosine π→π transition energies are below the electron detachment energy. Inter-strand π→π transitions of the excess electron from C to G are predicted to be less than 2.79 eV. Electron transfer might also be possible through the inter-strand base-jumping mode. An analysis of absorption visible spectra reveals the absorption bands ranging from 500 nm to 700 nm for the cytosine-rich radical anions of the DNA duplex. Electron attachment to cytidine oligomers might add color to the DNA duplex.
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Affiliation(s)
- Jiande Gu
- Drug Design & Discovery Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.
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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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37
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Wang S, Zhang C, Zhao P, Bu Y. Efficient and Substantial DNA Lesions From Near 0 eV Electron-Induced Decay of the O4-Hydrogenated Thymine Nucleotides: A DFT Study. J Phys Chem B 2015; 119:13971-9. [PMID: 26441346 DOI: 10.1021/acs.jpcb.5b06195] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Possible electron-induced ruptures of C3'-O3', C5'-O5', and N1-C1' bonds in O4-hydrogenated 2'-deoxythymidine-3'-monophosphate (3'-dT(O4H)MPH) and 2'-deoxythymidine-5'-monophosphate (5'-dT(O4H)MPH) are investigated using density functional theory calculations, and efficient pathways are proposed. Electron attachment causes remarkable structural relaxation in the thymine C6 site. A concerted process of intramolecular proton transfer (IPT) from the C2' site of 2'-deoxyribose to the C6 site and the C3'-O3' bond rupture is observed in [3'-dT(O4H)MPH](-). A low activation barrier (9.32 kcal/mol) indicates that this pathway is the most efficient one as compared to other known pathways leading to backbone breaks of a single strand DNA at the non-3'-end thymine, which prevents the N1-C1' bond cleavage in [3'-dT(O4H)MPH](-). However, essentially spontaneous N1-C1' bond cleavage following similar IPT is predicted in [5'-dT(O4H)MPH](-). A moderate activation barrier (13.02 kcal/mol) for the rate-controlling IPT step suggests that base release from the N1-C1' cleavage arises readily at the 3'-end of single strand DNA with the strand ended by a thymine. The C5'-O5' bond has only an insignificant change in the IPT process. Solvent effects are found to increase slightly the energy requirements for either bond ruptures (11.23 kcal/mol (C3'-O3') vs 16.18 kcal/mol (N1-C1')), but not change their relative efficiencies.
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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
| | - Changzhe Zhang
- 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
| | - Yuxiang Bu
- School of Chemistry and Chemical Engineering, Institute of Theoretical Chemistry, Shandong University , Jinan, 250100 P. R. China
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38
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Interference effects in the electron and positron scattering from molecules at intermediate and high energies. Chem Phys Lett 2015. [DOI: 10.1016/j.cplett.2015.06.066] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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39
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Sato K, Nishikino M, Kawachi T, Shimokawa T, Imai T, Teshima T, Nishimura H, Kando M. A laser-plasma-produced soft X-ray laser at 89 eV generates DNA double-strand breaks in human cancer cells. JOURNAL OF RADIATION RESEARCH 2015; 56:633-638. [PMID: 25862698 PMCID: PMC4497388 DOI: 10.1093/jrr/rrv015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Revised: 01/28/2015] [Accepted: 03/06/2015] [Indexed: 06/04/2023]
Abstract
While it has been expected that X-ray laser will be widely applied to biomedical studies, this has not been achieved to date and its biological effects such as DNA damage have not been evaluated. As a first step for its biological application, we developed a culture cell irradiation system, particularly designed for a plasma-driven soft X-ray laser pulse, to investigate whether the soft X-ray laser is able to induce DNA double strand breaks (DSBs) in living cells or not. The human adenocarcimona cell line A549 was irradiated with the soft X-ray laser at a photon energy of 89 eV and the repair focus formation of the DSBs was assessed by immunofluorescence staining with antiphosphorylated DNA-PKcs (p-DNA-PKcs), ATM (p-ATM) and γ-H2AX antibody. The p-DNA-PKcs, ATM, and γ-H2AX foci were clearly identified after soft X-ray laser irradiation. Furthermore, the increase in the X-ray laser shot number, even from a single shot, results in the increase in p-DNA-PKcs foci. These results are the first evidence that the 89 eV soft X-ray laser is able to induce DSB in living cells. Our study demonstrated that this irradiation system is a useful tool for investigating the radiobiological effect of soft X-ray laser.
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Affiliation(s)
- Katsutoshi Sato
- Cancer Metastasis Research Team, Advanced Radiation Biology Research Program, Research Center for Charged Particle Therapy, National Institute of Radiological Sciences, 4-9-1 Anagawa, Inage-ku, Chiba, 263-8555, Japan
| | - Masaharu Nishikino
- X-ray Laser Application Group, Quantum Beam Science Directorate, Kansai Photon Science Institute, Japan Atonic Energy Agency, 8-1-7 Umemidai, Kizugawa, Kyoto, 619-0215, Japan
| | - Tetsuya Kawachi
- X-ray Laser Application Group, Quantum Beam Science Directorate, Kansai Photon Science Institute, Japan Atonic Energy Agency, 8-1-7 Umemidai, Kizugawa, Kyoto, 619-0215, Japan
| | - Takashi Shimokawa
- Cancer Metastasis Research Team, Advanced Radiation Biology Research Program, Research Center for Charged Particle Therapy, National Institute of Radiological Sciences, 4-9-1 Anagawa, Inage-ku, Chiba, 263-8555, Japan
| | - Takashi Imai
- Advanced Radiation Biology Research Program, Research Center for Charged Particle Therapy, National Institute of Radiological Sciences, 4-9-1 Anagawa, Inage-ku, Chiba, 263-8555, Japan
| | - Teruki Teshima
- Department of Radiation Oncology, Osaka Medical Center for Cancer and Cardiovascular Diseases, 1-3-3 Nakamichi, Higashinari-ku, Osaka, 537-8511 Japan
| | - Hiroaki Nishimura
- Institute of Laser Engineering, Osaka University, 2-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Masaki Kando
- Laser Electron Accelerator Group, Quantum Beam Science Directorate, Kansai Photon Science Institute, Japan Atonic Energy Agency, 8-1-7 Umemidai, Kizugawa, Kyoto, 619-0215, Japan
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40
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Zhao J, Wang M, Fu A, Yang H, Bu Y. Hydrated Electron Transfer to Nucleobases in Aqueous Solutions Revealed by Ab Initio Molecular Dynamics Simulations. Chemphyschem 2015; 16:2348-56. [DOI: 10.1002/cphc.201500040] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Indexed: 11/07/2022]
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41
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Fasshauer E, Kolorenč P, Pernpointner M. Relativistic decay widths of autoionization processes: The relativistic FanoADC-Stieltjes method. J Chem Phys 2015; 142:144106. [DOI: 10.1063/1.4917255] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Elke Fasshauer
- Centre for Theoretical and Computational Chemistry, Department of Chemistry, University of Tromsø–The Arctic University of Norway, N-9037 Tromsø, Norway
- Theoretische Chemie, Universität Heidelberg, Im Neuenheimer Feld 229, D-69120 Heidelberg, Germany
| | - Přemysl Kolorenč
- Institute of Theoretical Physics, Faculty of Mathematics and Physics, Charles University in Prague, V Holešovičkách 2, 180 00 Prague, Czech Republic
| | - Markus Pernpointner
- Theoretische Chemie, Universität Heidelberg, Im Neuenheimer Feld 229, D-69120 Heidelberg, Germany
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42
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Minaev BF, Shafranyosh MI, Svida YY, Sukhoviya MI, Shafranyosh II, Baryshnikov GV, Minaeva VA. Fragmentation of the adenine and guanine molecules induced by electron collisions. J Chem Phys 2015; 140:175101. [PMID: 24811665 DOI: 10.1063/1.4871881] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Secondary electron emission is the most important stage in the mechanism of radiation damage to DNA biopolymers induced by primary ionizing radiation. These secondary electrons ejected by the primary electron impacts can produce further ionizations, initiating an avalanche effect, leading to genome damage through the energy transfer from the primary objects to sensitive biomolecular targets, such as nitrogenous bases, saccharides, and other DNA and peptide components. In this work, the formation of positive and negative ions of purine bases of nucleic acids (adenine and guanine molecules) under the impact of slow electrons (from 0.1 till 200 eV) is studied by the crossed electron and molecular beams technique. The method used makes it possible to measure the molecular beam intensity and determine the total cross-sections for the formation of positive and negative ions of the studied molecules, their energy dependences, and absolute values. It is found that the maximum cross section for formation of the adenine and guanine positive ions is reached at about 90 eV energy of the electron beam and their absolute values are equal to 2.8 × 10(-15) and 3.2 × 10(-15) cm(2), respectively. The total cross section for formation of the negative ions is 6.1 × 10(-18) and 7.6 × 10(-18) cm(2) at the energy of 1.1 eV for adenine and guanine, respectively. The absolute cross-section values for the molecular ions are measured and the cross-sections of dissociative ionization are determined. Quantum chemical calculations are performed for the studied molecules, ions and fragments for interpretation of the crossed beams experiments.
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Affiliation(s)
- B F Minaev
- Bohdan Khmelnitsky National University, 18031 Cherkasy, Ukraine
| | | | - Yu Yu Svida
- Uzhgorod National University, 88000 Uzhgorod, Ukraine
| | - M I Sukhoviya
- Uzhgorod National University, 88000 Uzhgorod, Ukraine
| | | | - G V Baryshnikov
- Bohdan Khmelnitsky National University, 18031 Cherkasy, Ukraine
| | - V A Minaeva
- Bohdan Khmelnitsky National University, 18031 Cherkasy, Ukraine
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43
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Alizadeh E, Orlando TM, Sanche L. Biomolecular damage induced by ionizing radiation: the direct and indirect effects of low-energy electrons on DNA. Annu Rev Phys Chem 2015; 66:379-98. [PMID: 25580626 DOI: 10.1146/annurev-physchem-040513-103605] [Citation(s) in RCA: 236] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Many experimental and theoretical advances have recently allowed the study of direct and indirect effects of low-energy electrons (LEEs) on DNA damage. In an effort to explain how LEEs damage the human genome, researchers have focused efforts on LEE interactions with bacterial plasmids, DNA bases, sugar analogs, phosphate groups, and longer DNA moieties. Here, we summarize the current understanding of the fundamental mechanisms involved in LEE-induced damage of DNA and complex biomolecule films. Results obtained by several laboratories on films prepared and analyzed by different methods and irradiated with different electron-beam current densities and fluencies are presented. Despite varied conditions (e.g., film thicknesses and morphologies, intrinsic water content, substrate interactions, and extrinsic atmospheric compositions), comparisons show a striking resemblance in the types of damage produced and their yield functions. The potential of controlling this damage using molecular and nanoparticle targets with high LEE yields in targeted radiation-based cancer therapies is also discussed.
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Affiliation(s)
- Elahe Alizadeh
- Groupe en Sciences des Radiations, Département de Médecine Nucléaire et Radiobiologie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, J1H 5N4 Sherbrooke, Canada
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44
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Kouass Sahbani S, Sanche L, Cloutier P, Bass AD, Hunting DJ. Loss of cellular transformation efficiency induced by DNA irradiation with low-energy (10 eV) electrons. J Phys Chem B 2014; 118:13123-31. [PMID: 25325149 DOI: 10.1021/jp508170c] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Low energy electrons (LEEs) of energies less than 20 eV are generated in large quantities by ionizing radiation in biological matter. While LEEs are known to induce single (SSBs) and double strand breaks (DSBs) in DNA, their ability to inactivate cells by inducing nonreparable lethal damage has not yet been demonstrated. Here we observe the effect of LEEs on the functionality of DNA, by measuring the efficiency of transforming Escherichia coli with a [pGEM-3Zf (-)] plasmid irradiated with 10 eV electrons. Highly ordered DNA films were prepared on pyrolitic graphite by molecular self-assembly using 1,3-diaminopropane ions (Dap(2+)). The uniformity of these films permits the inactivation of approximately 50% of the plasmids compared to <10% using previous methods, which is sufficient for the subsequent determination of their functionality. Upon LEE irradiation, the fraction of functional plasmids decreased exponentially with increasing electron fluence, while LEE-induced isolated base damage, frank DSB, and non DSB-cluster damage increased linearly with fluence. While DSBs can be toxic, their levels were too low to explain the loss of plasmid functionality observed upon LEE irradiation. Similarly, non-DSB cluster damage, revealed by transforming cluster damage into DSBs by digestion with repair enzymes, also occurred relatively infrequently. The exact nature of the lethal damage remains unknown, but it is probably a form of compact cluster damage in which the lesions are too close to be revealed by purified repair enzymes. In addition, this damage is either not repaired or is misrepaired by E. coli, since it results in plasmid inactivation, when they contain an average of three lesions. Comparison with previous results from a similar experiment performed with γ-irradiated plasmids indicates that the type of clustered DNA lesions, created directly on cellular DNA by LEEs, may be more difficult to repair than those produced by other species from radiolysis.
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Affiliation(s)
- Saloua Kouass Sahbani
- Department of Nuclear Medicine & Radiobiology, Faculty of Medicine, Université de Sherbrooke , Sherbrooke, Quebec, Canada J1H 5N4
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Ren X, Pflüger T, Weyland M, Baek WY, Rabus H, Ullrich J, Dorn A. An (e, 2e + ion) study of low-energy electron-impact ionization and fragmentation of tetrahydrofuran with high mass and energy resolutions. J Chem Phys 2014; 141:134314. [DOI: 10.1063/1.4896614] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
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Barbosa AS, Bettega MHF. Elastic scattering of low-energy electrons by 1,4-dioxane. J Chem Phys 2014; 140:184303. [PMID: 24832266 DOI: 10.1063/1.4874646] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We report calculated cross sections for elastic collisions of low-energy-electrons with 1,4-dioxane. Our calculations employed the Schwinger multichannel method with pseudopotentials and were carried out in the static-exchange and static-exchange plus polarization approximations for energies up to 30 eV. Our results show the presence of three shape resonances belonging to the Bu, Au, and Bg symmetries and located at 7.0 eV, 8.4 eV, and 9.8 eV, respectively. We also report the presence of a Ramsauer-Townsend minimum located at around 0.05 eV. We compare our calculated cross sections with experimental data and R-matrix and independent atom model along with the additivity rule corrected by using screening coefficients theoretical results for 1,4-dioxane obtained by Palihawadana et al. [J. Chem. Phys. 139, 014308 (2013)]. The agreement between the present and the R-matrix theoretical calculations of Palihawadana et al. is relatively good at energies below 10 eV. Our calculated differential cross sections agree well with the experimental data, showing only some discrepancies at higher energies.
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Affiliation(s)
- Alessandra Souza Barbosa
- Departamento de Física, Universidade Federal do Paraná, Caixa Postal 19044, 81531-990 Curitiba, Paraná, Brazil
| | - Márcio H F Bettega
- Departamento de Física, Universidade Federal do Paraná, Caixa Postal 19044, 81531-990 Curitiba, Paraná, Brazil
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Luo X, Zheng Y, Sanche L. DNA strand breaks and crosslinks induced by transient anions in the range 2-20 eV. J Chem Phys 2014; 140:155101. [PMID: 26792947 PMCID: PMC4716823 DOI: 10.1063/1.4870519] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The energy dependence of the yields of single and double strand breaks (SSB and DSB) and crosslinks induced by electron impact on plasmid DNA films is measured in the 2-20 eV range. The yield functions exhibit two strong maxima, which are interpreted to result from the formation of core-excited resonances (i.e., transient anions) of the bases, and their decay into the autoionization channel, resulting in π → π* electronic transitions of the bases followed by electron transfer to the C-O σ* bond in the phosphate group. Occupancy of the σ* orbital ruptures the C-O bond of the backbone via dissociative electron attachment, producing a SSB. From a comparison of our results with those of other works, including theoretical calculations and electron-energy-loss spectra of the bases, the 4.6 eV peak in the SSB yield function is attributed to the resonance decay into the lowest electronically excited states of the bases; in particular, those resulting from the transitions 13A'(π2 → π3*) and 13A″(n2 → π3*) of thymine and 13A'(π → π*) of cytosine. The strongest peak at 9.6 eV in the SSB yield function is also associated with electron captured by excited states of the bases, resulting mostly from a multitude of higher-energy π → π* transitions. The DSB yield function exhibits strong maxima at 6.1 and 9.6 eV. The peak at 9.6 eV is probably related to the same resonance manifold as that leading to SSB, but the other at 6.1 eV may be more restricted to decay into the electronic state 13A' (π → π*) of cytosine via autoionization. The yield function of crosslinks is dominated by a broad peak extending over the 3.6-11.6 eV range with a sharper one at 17.6 eV. The different line shape of the latter function, compared to that of SSB and DSB, appears to be due to the formation of reactive radical sites in the initial supercoiled configuration of the plasmid, which react with the circular form (i.e., DNA with a SSB) to produce a crosslink.
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Affiliation(s)
- Xinglan Luo
- Research Institute of Photocatalysis, State Key Laboratory of Photocatalysis on Energy and Environment, Fuzhou University, Fuzhou 350002, People’s Republic of China
| | - Yi Zheng
- Research Institute of Photocatalysis, State Key Laboratory of Photocatalysis on Energy and Environment, Fuzhou University, Fuzhou 350002, People’s Republic of China
| | - Léon Sanche
- Group in the Radiation Sciences, Faculty of Medicine, Université de Sherbrooke, Sherbrooke, Quebec J1H 5N4, Canada
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Dharmadhikari AK, Bharambe H, Dharmadhikari JA, D'Souza JS, Mathur D. DNA damage by OH radicals produced using intense, ultrashort, long wavelength laser pulses. PHYSICAL REVIEW LETTERS 2014; 112:138105. [PMID: 24745462 DOI: 10.1103/physrevlett.112.138105] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Indexed: 05/24/2023]
Abstract
We probe femtosecond laser induced damage to aqueous DNA, relying on strong-field interaction with water wherein electrons and free radicals are generated in situ; these, in turn, interact with DNA plasmids under physiological conditions, producing nicks. Exposure to intense femtosecond pulses of 1350 and 2200 nm light induces single strand breaks and double strand breaks (DSBs) in DNA. At the longer wavelength (and at higher intensities), rotationally hot OH radicals induce DSBs, producing linear DNA. Strand breaks occur due to single or multiple OH hits on DNA. With 2200 nm light, DSBs are formed mostly by the action of two OH radicals; use of OH scavengers establishes that the probability of a two-hit event reduces much faster than a one-hit event as scavenger concentration is increased. Thermal effects do not induce DSBs with 2200 nm light.
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Affiliation(s)
- A K Dharmadhikari
- Tata Institute of Fundamental Research, 1 Homi Bhabha Road, Mumbai 400 005, India
| | - H Bharambe
- UM-DAE Centre for Excellence in Basic Science, Kalina Campus, Santa Cruz (East), Mumbai 400 098, India
| | - J A Dharmadhikari
- Centre for Atomic and Molecular Physics, Manipal University, Manipal 576 104, India
| | - J S D'Souza
- UM-DAE Centre for Excellence in Basic Science, Kalina Campus, Santa Cruz (East), Mumbai 400 098, India
| | - D Mathur
- Tata Institute of Fundamental Research, 1 Homi Bhabha Road, Mumbai 400 005, India and Centre for Atomic and Molecular Physics, Manipal University, Manipal 576 104, India
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Gu J, Xie Y, Schaefer HF. Benchmarking the Electron Affinity of Uracil. J Chem Theory Comput 2014; 10:609-12. [DOI: 10.1021/ct400958d] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Jiande Gu
- Drug Design & Discovery Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, CAS, Shanghai 201203, People’s Republic of China
| | - Yaoming Xie
- Center for Computational
Quantum Chemistry, University of Georgia, Athens, Georgia 30602-2525, United States
| | - Henry F. Schaefer
- Center for Computational
Quantum Chemistry, University of Georgia, Athens, Georgia 30602-2525, United States
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Bacchus-Montabonel M. Anisotropy and charge effect in collisions of ions with biomolecules. Appl Radiat Isot 2014; 83 Pt B:95-9. [DOI: 10.1016/j.apradiso.2012.12.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2012] [Revised: 12/19/2012] [Accepted: 12/27/2012] [Indexed: 11/15/2022]
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