1932

Abstract

Ionizing rays cause damage to genomes, proteins, and signaling pathways that normally regulate cell activity, with harmful consequences such as accelerated aging, tumors, and cancers but also with beneficial effects in the context of radiotherapies. While the great pace of research in the twentieth century led to the identification of the molecular mechanisms for chemical lesions on the building blocks of biomacromolecules, the last two decades have brought renewed questions, for example, regarding the formation of clustered damage or the rich chemistry involving the secondary electrons produced by radiolysis. Radiation chemistry is now meeting attosecond science, providing extraordinary opportunities to unravel the very first stages of biological matter radiolysis. This review provides an overview of the recent progress made in this direction, focusing mainly on the atto- to femto- to picosecond timescales. We review promising applications of time-dependent density functional theory in this context.

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2021-04-20
2024-03-28
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Literature Cited

  1. 1. 
    Skłodowska Curie M. 1904. Recherches sur les Substances Radioactives Paris: Gauthier-Villars
  2. 2. 
    Hatano Y, Katsumura Y, Mozumder A. 2010. Introduction. Charged Particle and Photon Interactions with Matter1–7 Boca Raton, FL: CRC Press
    [Google Scholar]
  3. 3. 
    Dizdaroglu M, Jaruga P. 2012. Mechanisms of free radical-induced damage to DNA. Free Radic. Res. 46:4382–419
    [Google Scholar]
  4. 4. 
    Yamamori T, Yasui H, Yamazumi M, Wada Y, Nakamura Y et al. 2012. Ionizing radiation induces mitochondrial reactive oxygen species production accompanied by upregulation of mitochondrial electron transport chain function and mitochondrial content under control of the cell cycle checkpoint. Free Radic. Biol. Med. 53:2260–70
    [Google Scholar]
  5. 5. 
    Yoshida T, Goto S, Kawakatsu M, Urata Y, Li T. 2012. Mitochondrial dysfunction, a probable cause of persistent oxidative stress after exposure to ionizing radiation. Free Radic. Res. 46:2147–53
    [Google Scholar]
  6. 6. 
    Szumiel I. 2015. Ionizing radiation-induced oxidative stress, epigenetic changes and genomic instability: the pivotal role of mitochondria. Int. J. Radiat. Biol. 91:11–12
    [Google Scholar]
  7. 7. 
    Huber S, Butz L, Stegen B, Klumpp D, Braun N et al. 2013. Ionizing radiation, ion transports, and radioresistance of cancer cells. Front. Physiol. 4:212
    [Google Scholar]
  8. 8. 
    Stark G. 2005. Functional consequences of oxidative membrane damage. J. Membr. Biol. 205:11–16
    [Google Scholar]
  9. 9. 
    Cucinotta FA, Durante M 2006. Cancer risk from exposure to galactic cosmic rays: implications for space exploration by human beings. Lancet Oncol 7:5431–35
    [Google Scholar]
  10. 10. 
    Kuncic Z, Lacombe S. 2018. Nanoparticle radio-enhancement: principles, progress and application to cancer treatment. Phys. Med. Biol. 63:202TR01
    [Google Scholar]
  11. 11. 
    Kamada T, Tsujii H, Blakely EA, Debus J, De Neve W et al. 2015. Carbon ion radiotherapy in Japan: an assessment of 20 years of clinical experience. Lancet Oncol 16:2e93–100
    [Google Scholar]
  12. 12. 
    Lacombe S, Porcel E, Scifoni E. 2017. Particle therapy and nanomedicine: state of art and research perspectives. Cancer Nanotechnol 8:19
    [Google Scholar]
  13. 13. 
    Lorat Y, Brunner CU, Schanz S, Jakob B, Taucher-Scholz G, Rübe CE 2015. Nanoscale analysis of clustered DNA damage after high-LET irradiation by quantitative electron microscopy—the heavy burden to repair. DNA Repair 28:93–106
    [Google Scholar]
  14. 14. 
    Sage E, Shikazono N. 2017. Radiation-induced clustered DNA lesions: repair and mutagenesis. Oxidative DNA Damage Repair 107:125–35
    [Google Scholar]
  15. 15. 
    Mavragani IV, Nikitaki Z, Souli MP, Aziz A, Nowsheen S et al. 2017. Complex DNA damage: a route to radiation-induced genomic instability and carcinogenesis. Cancers 9:791
    [Google Scholar]
  16. 16. 
    Kakarougkas A, Jeggo PA. 2014. DNA DSB repair pathway choice: an orchestrated handover mechanism. Br. J. Radiol. 87: 1035.20130685
    [Google Scholar]
  17. 17. 
    Asaithamby A, Hu B, Chen DJ. 2011. Unrepaired clustered DNA lesions induce chromosome breakage in human cells. PNAS 108:208293–98
    [Google Scholar]
  18. 18. 
    Lukas J, Lukas C, Bartek J. 2011. More than just a focus: the chromatin response to DNA damage and its role in genome integrity maintenance. Nat. Cell Biol. 13:101161–69
    [Google Scholar]
  19. 19. 
    Wilson MD, Benlekbir S, Fradet-Turcotte A, Sherker A, Julien J-P et al. 2016. The structural basis of modified nucleosome recognition by 53BP1. Nature 536:100–3
    [Google Scholar]
  20. 20. 
    Boudaïffa B, Cloutier P, Hunting D, Huels MA, Sanche L. 2000. Resonant formation of DNA strand breaks by low-energy (3 to 20 eV) electrons. Science 287:54581658–60
    [Google Scholar]
  21. 21. 
    Alizadeh E, Orlando TM, Sanche L. 2015. Biomolecular damage induced by ionizing radiation: the direct and indirect effects of low-energy electrons on DNA. Annu. Rev. Phys. Chem. 66:379–98
    [Google Scholar]
  22. 22. 
    Dong Y, Gao Y, Liu W, Gao T, Zheng Y, Sanche L. 2019. Clustered DNA damage induced by 2–20 eV electrons and transient anions: general mechanism and correlation to cell death. J. Phys. Chem. Lett. 10:112985–90
    [Google Scholar]
  23. 23. 
    Ma J, Wang F, Denisov SA, Adhikary A, Mostafavi M. 2017. Reactivity of prehydrated electrons toward nucleobases and nucleotides in aqueous solution. Sci. Adv. 3:12e1701669
    [Google Scholar]
  24. 24. 
    Ma J, Kumar A, Muroya Y, Yamashita S, Sakurai T et al. 2019. Observation of dissociative quasi-free electron attachment to nucleoside via excited anion radical in solution. Nat. Commun. 10:1102
    [Google Scholar]
  25. 25. 
    Arumainayagam CR, Garrod RT, Boyer MC, Hay AK, Bao ST et al. 2019. Extraterrestrial prebiotic molecules: photochemistry versus radiation chemistry of interstellar ices. Chem. Soc. Rev. 48:82293–314
    [Google Scholar]
  26. 26. 
    Bennett CJ, Pirim C, Orlando TM. 2013. Space-weathering of solar system bodies: a laboratory perspective. Chem. Rev. 113:129086–150
    [Google Scholar]
  27. 27. 
    Nass K. 2019. Radiation damage in protein crystallography at X-ray free-electron lasers. Acta Crystallogr. Sect. D 75:2211–18
    [Google Scholar]
  28. 28. 
    Bury C, Garman EF, Ginn HM, Ravelli RBG, Carmichael I et al. 2015. Radiation damage to nucleoprotein complexes in macromolecular crystallography. J. Synchrotron Radiat. 22:213–24
    [Google Scholar]
  29. 29. 
    Loh Z-H, Doumy G, Arnold C, Kjellsson L, Southworth SH et al. 2020. Observation of the fastest chemical processes in the radiolysis of water. Science 367:6474179
    [Google Scholar]
  30. 30. 
    Trinter F, Schöffler MS, Kim H-K, Sturm FP, Cole K et al. 2014. Resonant Auger decay driving intermolecular Coulombic decay in molecular dimers. Nature 505:7485664–66
    [Google Scholar]
  31. 31. 
    Calegari F, Ayuso D, Trabattoni A, Belshaw L, De Camillis S et al. 2014. Ultrafast electron dynamics in phenylalanine initiated by attosecond pulses. Science 346:6207336
    [Google Scholar]
  32. 32. 
    Belloni J, Monard H, Gobert F, Larbre J-P, Demarque A et al. 2005. ELYSE—a picosecond electron accelerator for pulse radiolysis research. Nucl. Instrum. Methods Phys. Res. Sect. A 539:3527–39
    [Google Scholar]
  33. 33. 
    Thürmer S, Ončák M, Ottosson N, Seidel R, Hergenhahn U et al. 2013. On the nature and origin of dicationic, charge-separated species formed in liquid water on X-ray irradiation. Nat. Chem. 5:7590–96
    [Google Scholar]
  34. 34. 
    Dinh PM, du Bourg LB, Gao C-Z, Gu B, Lacombe L et al. 2017. On the quantum description of irradiation dynamics in systems of biological relevance. Nanoscale Insights into Ion-Beam Cancer Therapy AV Solov'yov 277–309 Cham, Switz: Springer Int.
    [Google Scholar]
  35. 35. 
    Kohanoff J, McAllister M, Tribello GA, Gu B. 2017. Interactions between low energy electrons and DNA: a perspective from first-principles simulations. J. Phys. Condens. Matter 29:38383001
    [Google Scholar]
  36. 36. 
    Gu J, Leszczynski J, Schaefer HF. 2012. Interactions of electrons with bare and hydrated biomolecules: from nucleic acid bases to DNA segments. Chem. Rev. 112:115603–40
    [Google Scholar]
  37. 37. 
    Monari A, Dumont E. 2015. Understanding DNA under oxidative stress and sensitization: the role of molecular modeling. Front. Chem. 3:43
    [Google Scholar]
  38. 38. 
    Tavernelli I. 2015. Nonadiabatic molecular dynamics simulations: synergies between theory and experiments. Acc. Chem. Res. 48:3792–800
    [Google Scholar]
  39. 39. 
    Parise A, Alvarez-Ibarra A, Wu X, Zhao X, Pilmé J, de la Lande A. 2018. Quantum chemical topology of the electron localization function in the field of attosecond electron dynamics. J. Phys. Chem. Lett. 9:4844–50
    [Google Scholar]
  40. 40. 
    Howell RW. 2008. Auger processes in the 21st century. Int. J. Radiat. Biol. 84:12959–75
    [Google Scholar]
  41. 41. 
    Cederbaum LS, Zobeley J, Tarantelli F. 1997. Giant intermolecular decay and fragmentation of clusters. Phys. Rev. Lett. 79:244778–81
    [Google Scholar]
  42. 42. 
    von Sonntag C. 2010. Radiation-induced DNA damage: indirect effects. Recent Trends in Radiation Chemistry JF Wishart 543–62 London: World Scientific
    [Google Scholar]
  43. 43. 
    Becker D, Adhikary A, Sevilla MD. 2010. Mechanisms of radiation-induced DNA damage: direct effects. Recent Trends in Radiation Chemistry JF Wishart 509–42 London: World Scientific
    [Google Scholar]
  44. 44. 
    LaVere T, Becker D, Sevilla MD. 1996. Yields of OH in gamma-irradiated DNA as a function of DNA hydration: hole transfer in competition OH formation. Radiat Res 145:673
    [Google Scholar]
  45. 45. 
    Cederbaum LS, Zobeley J. 1999. Ultrafast charge migration by electron correlation. Chem. Phys. Lett. 307:3205–10
    [Google Scholar]
  46. 46. 
    Friedland W, Dingfelder M, Kundrát P, Jacob P. 2011. Track structures, DNA targets and radiation effects in the biophysical Monte Carlo simulation code PARTRAC. Mutat. Res. 711:1–228–40
    [Google Scholar]
  47. 47. 
    Francis Z, Incerti S, Karamitros M, Tran HN, Villagrasa C. 2011. Stopping power and ranges of electrons, protons and alpha particles in liquid water using the Geant4-DNA package. Nucl. Instrum. Methods Phys. Res. Sect. B 269:202307–11
    [Google Scholar]
  48. 48. 
    Marante C, Klinker M, Corral I, González-Vázquez J, Argenti L, Martín F. 2017. Hybrid-basis close-coupling interface to quantum chemistry packages for the treatment of ionization problems. J. Chem. Theory Comput. 13:2499–514
    [Google Scholar]
  49. 49. 
    Jagau T-C, Bravaya KB, Krylov AI. 2017. Extending quantum chemistry of bound states to electronic resonances. Annu. Rev. Phys. Chem. 68:525–53
    [Google Scholar]
  50. 50. 
    Miteva T, Kazandjian S, Sisourat N. 2017. On the computations of decay widths of Fano resonances. Chem. Phys. 482:208–15
    [Google Scholar]
  51. 51. 
    Whitenack DL, Wasserman A. 2011. Density functional resonance theory of unbound electronic systems. Phys. Rev. Lett. 107:16163002
    [Google Scholar]
  52. 52. 
    Runge E, Gross EKU. 1984. Density-functional theory for time-dependent systems. Phys. Rev. Lett. 52:12997–1000
    [Google Scholar]
  53. 53. 
    Calvayrac F, Reinhard PG, Suraud E. 1995. Nonlinear plasmon response in highly excited metallic clusters. Phys. Rev. B. 52:24R17056–59
    [Google Scholar]
  54. 54. 
    Yabana K, Bertsch GF. 1996. Time-dependent local-density approximation in real time. Phys. Rev. B. 54:74484–87
    [Google Scholar]
  55. 55. 
    Flick J, Ruggenthaler M, Appel H, Rubio A. 2015. Kohn-Sham approach to quantum electrodynamical density-functional theory: exact time-dependent effective potentials in real space. PNAS 112:5015285
    [Google Scholar]
  56. 56. 
    Wu X, Alvarez-Ibarra A, Salahub DR, de la Lande A. 2018. Retardation in electron dynamics simulations based on time-dependent density functional theory. Eur. Phys. J. D 72:12206
    [Google Scholar]
  57. 57. 
    Rizzi V, Todorov TN, Kohanoff JJ. 2017. Inelastic electron injection in a water chain. Sci. Rep. 7:145410
    [Google Scholar]
  58. 58. 
    Schild A, Gross EKU. 2017. Exact single-electron approach to the dynamics of molecules in strong laser fields. Phys. Rev. Lett. 118:16163202
    [Google Scholar]
  59. 59. 
    Zhao L, Tao Z, Pavošević F, Wildman A, Hammes-Schiffer S, Li X. 2020. Real-time time-dependent nuclear−electronic orbital approach: dynamics beyond the Born–Oppenheimer approximation. J. Phys. Chem. Lett. 11:104052–58
    [Google Scholar]
  60. 60. 
    Castro A, Marques MAL, Rubio A. 2004. Propagators for the time-dependent Kohn-Sham equations. J. Chem. Phys. 121:83425–33
    [Google Scholar]
  61. 61. 
    Gómez Pueyo A, Marques MAL, Rubio A, Castro A 2018. Propagators for the time-dependent Kohn-Sham equations: multistep, Runge-Kutta, exponential Runge-Kutta, and commutator free Magnus methods. J. Chem. Theory Comput. 14:63040–52
    [Google Scholar]
  62. 62. 
    Schleife A, Draeger EW, Anisimov VM, Correa AA, Kanai Y. 2014. Quantum dynamics simulation of electrons in materials on high-performance computers. Comput. Sci. Eng. 16:554–60
    [Google Scholar]
  63. 63. 
    Andrade X, Strubbe D, De Giovannini U, Larsen AH, Oliveira MJT et al. 2015. Real-space grids and the Octopus code as tools for the development of new simulation approaches for electronic systems. Phys. Chem. Chem. Phys. 17:4731371–96
    [Google Scholar]
  64. 64. 
    Kühne TD, Iannuzzi M, Del Ben M, Rybkin VV, Seewald P et al. 2020. CP2K: an electronic structure and molecular dynamics software package – Quickstep: efficient and accurate electronic structure calculations. J. Chem. Phys. 152:19194103
    [Google Scholar]
  65. 65. 
    Köster AM, Reveles JU, del Campo JM. 2004. Calculation of exchange-correlation potentials with auxiliary function densities. J. Chem. Phys. 121:83417–24
    [Google Scholar]
  66. 66. 
    Dunlap BI, Rösch N, Trickey SB. 2010. Variational fitting methods for electronic structure calculations. Mol. Phys. 108:21–233167–80
    [Google Scholar]
  67. 67. 
    The 26emon dev. 2019. deMon2k: a software package for density functional theory (DFT) calculations. . deMon2k. http://www.demon-software.com/public_html/index.html
    [Google Scholar]
  68. 68. 
    Mejía-Rodríguez D, Köster AM. 2014. Robust and efficient variational fitting of Fock exchange. J. Chem. Phys. 141:12124114
    [Google Scholar]
  69. 69. 
    Delesma FA, Geudtner G, Mejía-Rodríguez D, Calaminici P, Köster AM. 2018. Range-separated hybrid functionals with variational fitted exact exchange. J. Chem. Theory Comput. 14:115608–16
    [Google Scholar]
  70. 70. 
    de la Lande A, Clavaguéra C, Köster A. 2017. On the accuracy of population analyses based on fitted densities. J. Mol. Model. 23:499
    [Google Scholar]
  71. 71. 
    Choi J, Demmel J, Dhillon I, Dongarra J, Ostrouchov S et al. 1996. ScaLAPACK: a portable linear algebra library for distributed memory computers—design issues and performance. Comp. Phys. Comm. 97:1–2):1–15
    [Google Scholar]
  72. 72. 
    de la Lande A, Alvarez-Ibarra A, Hasnaoui K, Cailliez F, Wu X et al. 2019. Molecular simulations with in-deMon2k QM/MM, a tutorial-review. Molecules 24:91653
    [Google Scholar]
  73. 73. 
    Wu X, Teuler J-M, Cailliez F, Clavaguéra C, Salahub DR, de la Lande A. 2017. Simulating electron dynamics in polarizable environments. J. Chem. Theory Comput. 13:93985–4002
    [Google Scholar]
  74. 74. 
    Li X, Tully JC, Schlegel HB, Frisch MJ. 2005. Ab initio Ehrenfest dynamics. J. Chem. Phys. 123:8084106
    [Google Scholar]
  75. 75. 
    Tavernelli I, Röhrig UF, Rothlisberger U. 2005. Molecular dynamics in electronically excited states using time-dependent density functional theory. Mol. Phys. 103:6–8963–81
    [Google Scholar]
  76. 76. 
    Schleife A, Kanai Y, Correa AA. 2015. Accurate atomistic first-principles calculations of electronic stopping. Phys. Rev. B 91:1014306
    [Google Scholar]
  77. 77. 
    IAEA (Int. At. Energy Agency). 2020. Electronic Stopping Power of Matter for Ions Nucl. Data Serv.: Graphs, Data, Comments and Programs, Vienna, Austria, updated Feb. 20. https://www-nds.iaea.org/stopping/
  78. 78. 
    Ziegler JF. 2016. SRIM - The Stopping and Range of Ions in Matter. Interactions of Ions with Matter http://srim.org
    [Google Scholar]
  79. 79. 
    Mozumder A, Hatano Y. 2004. Charged Particle and Photon Interactions with Matter New York: Marcel Dekker
  80. 80. 
    Shukri AA, Bruneval F, Reining L. 2016. Ab initio electronic stopping power of protons in bulk materials. Phys. Rev. B 93:3035128
    [Google Scholar]
  81. 81. 
    Maliyov I, Crocombette J-P, Bruneval F. 2020. Quantitative electronic stopping power from localized basis set. Phys. Rev. B 101:3035136
    [Google Scholar]
  82. 82. 
    Correa AA. 2018. Calculating electronic stopping power in materials from first principles. Comput. Mater. Sci. 150:291–303
    [Google Scholar]
  83. 83. 
    Yost DC, Yao Y, Kanai Y. 2017. Examining real-time time-dependent density functional theory nonequilibrium simulations for the calculation of electronic stopping power. Phys. Rev. B 96:11115134
    [Google Scholar]
  84. 84. 
    Yu HS, Li SL, Truhlar DG. 2016. Perspective: Kohn-Sham density functional theory descending a staircase. J. Chem. Phys. 145:13130901
    [Google Scholar]
  85. 85. 
    Fuks JI, Lacombe L, Nielsen SEB, Maitra NT. 2018. Exploring non-adiabatic approximations to the exchange-correlation functional of TDDFT. Phys. Chem. Chem. Phys. 20:4126145–60
    [Google Scholar]
  86. 86. 
    Ullrich CA, Yang Z. 2014. A brief compendium of time-dependent density functional theory. Braz. J. Phys. 44:1154–88
    [Google Scholar]
  87. 87. 
    Dinh PM, Lacombe L, Reinhard P-G, Suraud É, Vincendon M. 2018. On the inclusion of dissipation on top of mean-field approaches. Eur. Phys. J. B 91:10246
    [Google Scholar]
  88. 88. 
    Privett AJ, Teixeira ES, Stopera C, Morales JA. 2017. Exploring water radiolysis in proton cancer therapy: time-dependent, non-adiabatic simulations of H+ + (H2O)1–6. PLOS ONE 12:4e0174456
    [Google Scholar]
  89. 89. 
    Reeves KG, Kanai Y. 2017. Electronic excitation dynamics in liquid water under proton irradiation. Sci. Rep. 7:140379
    [Google Scholar]
  90. 90. 
    Yost DC, Kanai Y. 2019. Electronic excitation dynamics in DNA under proton and α-particle irradiation. J. Am. Chem. Soc. 141:135241–51
    [Google Scholar]
  91. 91. 
    Alvarez-Ibarra A, Parise A, Hasnaoui K, de la Lande A. 2020. The physical stage of radiolysis of solvated DNA by high-energy-transfer particles: insights from new first principles simulations. Phys. Chem. Chem. Phys. 22:157747–58
    [Google Scholar]
  92. 92. 
    Trabattoni A, Galli M, Lara-Astiaso M, Palacios A, Greenwood J et al. 2019. Charge migration in photo-ionized aromatic amino acids. Philos. Trans. R. Soc. A 377:214520170472
    [Google Scholar]
  93. 93. 
    Lara-Astiaso M, Galli M, Trabattoni A, Palacios A, Ayuso D et al. 2018. Attosecond pump-probe spectroscopy of charge dynamics in tryptophan. J. Phys. Chem. Lett. 9:164570–77
    [Google Scholar]
  94. 94. 
    Rozzi CA, Falke SM, Spallanzani N, Rubio A, Molinari E et al. 2013. Quantum coherence controls the charge separation in a prototypical artificial light-harvesting system. Nat. Commun. 4:1602
    [Google Scholar]
  95. 95. 
    Vacher M, Bearpark MJ, Robb MA, Malhado JP. 2017. Electron dynamics upon ionization of polyatomic molecules: coupling to quantum nuclear motion and decoherence. Phys. Rev. Lett. 118:8083001
    [Google Scholar]
  96. 96. 
    Polyak I, Jenkins AJ, Vacher M, Bouduban MEF, Bearpark MJ, Robb MA. 2018. Charge migration engineered by localisation: electron-nuclear dynamics in polyenes and glycine. Mol. Phys. 116:19–202474–89
    [Google Scholar]
  97. 97. 
    Nijjar P, Jankowska J, Prezhdo OV. 2019. Ehrenfest and classical path dynamics with decoherence and detailed balance. J. Chem. Phys. 150:20204124
    [Google Scholar]
  98. 98. 
    Min SK, Agostini F, Tavernelli I, Gross EKU. 2017. Ab initio nonadiabatic dynamics with coupled trajectories: a rigorous approach to quantum (de)coherence. J. Phys. Chem. Lett. 8:133048–55
    [Google Scholar]
  99. 99. 
    Cai Z, Chen S, Wang L-W. 2019. Dissociation path competition of radiolysis ionization-induced molecule damage under electron beam illumination. Chem. Sci. 10:4610706–15
    [Google Scholar]
  100. 100. 
    Geerlings P, Chamorro E, Chattaraj PK, De Proft F, Gázquez JL et al. 2020. Conceptual density functional theory: status, prospects, issues. Theor. Chem. Acc. 139:236
    [Google Scholar]
  101. 101. 
    Chauvin R, Lepetit C, Silvi B, Alikhani E 2016. Challenges and Advances in Computational Chemistry and Physics, Vol. 22 Applications of Topological Methods in Molecular Chemistry Cham, Switz: Springer Int.
  102. 102. 
    Pilmé J, Luppi E, Bergès J, Houée-Lévin C, de la Lande A. 2014. Topological analyses of time-dependent electronic structures: application to electron-transfers in methionine enkephalin. J. Mol. Model. 20:82368
    [Google Scholar]
  103. 103. 
    Burnus T, Marques MAL, Gross EKU. 2005. Time-dependent electron localization function. Phys. Rev. A 71:1010501
    [Google Scholar]
  104. 104. 
    Schnitker J, Rossky PJ. 1987. Quantum simulation study of the hydrated electron. J. Chem. Phys. 86:63471–85
    [Google Scholar]
  105. 105. 
    Nicolas C, Boutin A, Lévy B, Borgis D. 2003. Molecular simulation of a hydrated electron at different thermodynamic state points. J. Chem. Phys. 118:219689–96
    [Google Scholar]
  106. 106. 
    Savolainen J, Uhlig F, Ahmed S, Hamm P, Jungwirth P. 2014. Direct observation of the collapse of the delocalized excess electron in water. Nat. Chem. 6:8697–701
    [Google Scholar]
  107. 107. 
    Li X, Sevilla MD, Sanche L. 2003. Density functional theory studies of electron interaction with DNA: can zero eV electrons induce strand breaks?. J. Am. Chem. Soc. 125:4513668–69
    [Google Scholar]
  108. 108. 
    Schyman P, Laaksonen A. 2008. On the effect of low-energy electron induced DNA strand break in aqueous solution: a theoretical study indicating guanine as a weak link in DNA. J. Am. Chem. Soc. 130:3712254–55
    [Google Scholar]
  109. 109. 
    Chen H-Y, Yang P-Y, Chen H-F, Kao C-L, Liao L-W 2014. DFT reinvestigation of DNA strand breaks induced by electron attachment. J. Phys. Chem. B 118:3811137–44
    [Google Scholar]
  110. 110. 
    Li X, Sanche L, Sevilla MD. 2006. Base release in nucleosides induced by low-energy electrons: a DFT study. Radiat. Res. 165:6721–29
    [Google Scholar]
  111. 111. 
    Kumar A, Becker D, Adhikary A, Sevilla MD. 2019. Reaction of electrons with DNA: radiation damage to radiosensitization. Int. J. Mol. Sci. 20:163998
    [Google Scholar]
  112. 112. 
    Smyth M, Kohanoff J. 2011. Excess electron localization in solvated DNA bases. Phys. Rev. Lett. 106:23238108
    [Google Scholar]
  113. 113. 
    McAllister M, Smyth M, Gu B, Tribello GA, Kohanoff J. 2015. Understanding the interaction between low-energy electrons and DNA nucleotides in aqueous solution. J. Phys. Chem. Lett. 6:153091–97
    [Google Scholar]
  114. 114. 
    Gu B, Smyth M, Kohanoff J. 2014. Protection of DNA against low-energy electrons by amino acids: a first-principles molecular dynamics study. Phys. Chem. Chem. Phys. 16:4424350–58
    [Google Scholar]
  115. 115. 
    Marsalek O, Elles CG, Pieniazek PA, Pluhařová E, VandeVondele J et al. 2011. Chasing charge localization and chemical reactivity following photoionization in liquid water. J. Chem. Phys. 135:22224510
    [Google Scholar]
  116. 116. 
    Wang F, Schmidhammer U, de La Lande A, Mostafavi M. 2017. Ultra-fast charge migration competes with proton transfer in the early chemistry of H2+. Phys. Chem. Chem. Phys. 19:42894–99
    [Google Scholar]
  117. 117. 
    López-Tarifa P, Gaigeot M-P, Vuilleumier R, Tavernelli I, Alcamí M et al. 2013. Ultrafast damage following radiation-induced oxidation of uracil in aqueous solution. Angew. Chem. Int. Ed. 52:113160–63
    [Google Scholar]
  118. 118. 
    López-Tarifa P, du Penhoat M-AH, Vuilleumier R, Gaigeot M-P, Tavernelli I et al. 2012. Ultrafast non-adiabatic fragmentation dynamics of doubly charged uracil in gas and liquid phase. J. Phys. Conf. Ser. 388:10102055
    [Google Scholar]
  119. 119. 
    López-Tarifa P, du Penhoat M-AH, Vuilleumier R, Gaigeot M-P, Tavernelli I et al. 2011. Ultrafast nonadiabatic fragmentation dynamics of doubly charged uracil in a gas phase. Phys. Rev. Lett. 107:2023202
    [Google Scholar]
  120. 120. 
    du Penhoat M-AH, Moraga NR, Gaigeot M-P, Vuilleumier R, Tavernelli I, Politis M-F. 2018. Proton collision on deoxyribose originating from doubly ionized water molecule dissociation. J. Phys. Chem. A 122:245311–20
    [Google Scholar]
  121. 121. 
    López-Tarifa P, Grzegorz D, Piekarski Rossich E, du Penhoat M-AH et al. 2014. Ultrafast nonadiabatic fragmentation dynamics of biomolecules. J. Phys. Conf. Ser. 488:1012037
    [Google Scholar]
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