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Chin. Phys. B, 2022, Vol. 31(6): 063401    DOI: 10.1088/1674-1056/ac4900

Collision site effect on the radiation dynamics of cytosine induced by proton

Xu Wang(王旭)1, Zhi-Ping Wang(王志萍)1,†, Feng-Shou Zhang(张丰收)2, and Chao-Yi Qian (钱超义)1
1 Department of Fundamental Courses, Wuxi Institute of Technology, Wuxi 214121, China;
2 The Key Laboratory of Beam Technology and Material Modification of Ministry of Education, College of Nuclear Science and Technology, Beijing Normal University, Beijing 100875, China
Abstract  By combing the time-dependent density functional calculations for electrons with molecular dynamics simulations for ions (TDDFT-MD) nonadiabatically in real time, we investigate the microscopic mechanism of collisions between cytosine and low-energy protons with incident energy ranging from 150 eV to 1000 eV. To explore the effects of the collision site and the proton incident energy on irradiation processes of cytosine, two collision sites are specially considered, which are N and O both acting as the proton receptors when forming hydrogen bonds with guanine. Not only the energy loss and the scattering angle of the projectile but also the electronic and ionic degrees of freedom of the target are identified. It is found that the energy loss of proton increases linearly with the increase of the incident energy in both situations, which are 14.2% and 21.1% of the incident energy respectively. However, the scattering angles show different behaviors in these two situations when the incident kinetic energy increases. When proton collides with O, the scattering angle of proton is larger and the energy lost is more, while proton captures less electrons from O. The calculated fragment mass distribution shows the high counts of the fragment mass of 1, implying the production of H+ fragment ion from cytosine even for proton with the incident energy lower than keV. Furthermore, the calculated results show that N on cytosine is easier to be combined with low-energy protons to form NH bonds than O.
Keywords:  time-dependent density functional theory      cytosine      proton-induced collision      fragmentation  
Received:  04 October 2021      Revised:  23 December 2021      Accepted manuscript online:  07 January 2022
PACS:  34.50.Gb (Electronic excitation and ionization of molecules)  
  82.30.Fi (Ion-molecule, ion-ion, and charge-transfer reactions)  
  87.15.H- (Dynamics of biomolecules)  
Fund: This work was supported by the National Natural Science Foundation of China (Grant Nos. 11905160 and 11635003), the ‘333’ Project of Jiangsu Province, China (Grant No. BRA2020327), the Science Foundation of Wuxi Institute of Technology (Grant No. ZK201903).
Corresponding Authors:  Zhi-Ping Wang     E-mail:

Cite this article: 

Xu Wang(王旭), Zhi-Ping Wang(王志萍), Feng-Shou Zhang(张丰收), and Chao-Yi Qian (钱超义) Collision site effect on the radiation dynamics of cytosine induced by proton 2022 Chin. Phys. B 31 063401

[1] Goodhead D T 1994 Int. J. Radiat. Biol. 65 7
[2] Von Sonntag C 2006 Free-Radical-Induced DNA Damage and Its Repair (Berlin: Springer)
[3] Boudaïffa B, Cloutier P, Hunting D, Huels M A and Sanche L 2000 Science 287 1658
[4] Fokas E, Kraft G, An H X and Engenhart-Cabillic R 2009 Biochim. Biophys. Acta 1796 216
[5] Reisz J A, Bansal N, Qian J, Zhao W L and Furdui C M 2014 Antioxid. Redox Signal. 21 260
[6] Friedland W, Schmitt E, Kundrát P, Dingfelder M, Baiocco G, Barbieri S and Ottolenghi A 2017 Sci. Rep. 7 45161
[7] Dong Y F, Liao H, Gao Y X, Cloutier P, Zheng Y and Sanche L 2021 J. Phys. Chem. Lett. 12 717
[8] Keta O, Petković V, Cirrone P, Petringa G, Cuttone G, Sakata D, Shin Wook-Geun, Incerti S, Petković I and Fira A R 2021 Int. J. Rad. Biol. 97 1229
[9] Tabet J, Eden S, Feil S, Abdoul-Carime H, Farizon B, Farizon M, Ouaskit S and Märk T D 2010 Phys. Rev. A 82 022703
[10] Ren X G, Wang E L, Skitnevskaya A D, Trofimov A B, Gokhberg K and Dorn A 2018 Nat. Phys. 14 1062
[11] Brédy R, Bernard J, Chen L, Wei B, Salmoun A, Bouchama T, Buchet-Poulizac M C and Martin S 2005 Nucl. Instrum. Methods. Phys. Res. Sect. B 235 392
[12] Dal Cappello C, Hervieux P A, Charpentier I and Ruiz-Lopez F 2008 Phys. Rev. A 78 042702
[13] Poully J C, Miles J, De Camillis S, Cassimi A and Greenwood J B 2015 Phys. Chem. Chem. Phys. 17 7172
[14] Sadr-Arani L, Mignon P, Chermette H, Abdoul-Carime H, Farizon B and Farizon M 2015 Phys. Chem. Chem. Phys. 17 11813
[15] Alvarez-Ibarra A, Parise A, Hasnaoui K and De la Lande A 2020 Phys. Chem. Chem. Phys. 22 7747
[16] Chowdhury M R, Mandal A, Bhogale A, Bansal H, Bagdia C, Bhattacharjee S, Monti J M, Rivarola R D and Tribedi L C 2020 Phys. Rev. A 102 012819
[17] Runge E and Gross E K U 1984 Phys. Rev. Lett. 52 997
[18] Sugino O and Miyamoto Y 1999 Phys. Rev. B 59 2579
[19] Seraide R, Bernal M A, Brunetto G, De Giovannini U and Rubio A 2017 J. Phys. Chem. B 121 7276
[20] Covington C, Hartig K, Russakoff A, Kulpins R and Varga K 2017 Phys. Rev. A 95 052701
[21] Yu W D, Gao C Z, Sato S A, Castro A, Rubio A and Wei B R 2021 Phys. Rev. A 103 032816
[22] Wang Z P, Zhang F S, Xu X F, Wang Y B and Qian C Y 2019 Mod. Phys. Lett. B 33 1950257
[23] Hong X H, Wang F, Wu Y, Gou B C and Wang J G 2016 Phys. Rev. A 93 062706
[24] Wang Z P, Dinh P M, Reinhard P G, Suraud E, Bruny G, Montano C, Feil S, Eden S, Abdoul-Carime H, Farizon B, Farizon M, Ouaskit S and Märk T D 2011 Int. J. Mass. Spectrom. 285 143
[25] Krasheninnikov A V, Miyamoto Y and Tománek D 2007 Phys. Rev. Lett. 99 016104
[26] Gao C Z, Wang J, Wang F and Zhang F S 2014 J. Chem. Phys 140 054308
[27] See about the TDDFT-MD model
[28] Dinh P M, Vincendon M, Coppens F, Suraud E and Reinhard P G 2022 Computer Phys. Comm. 270 108155
[29] Calvayrac F, Reinhard P G, Suraud E and Ullrich C A 2000 Phys. Rep. 337 493
[30] Zhao R T, Zhang N and Zhang F S 2018 Mol. Phys. 116 231
[31] Yu W, Gao C Z, Zhang Y, Zhang F S, Hutton R, Zou Y and Wei B 2018 Phys. Rev. A 97 032706
[32] Fennel Th, Meiwes-Broer K H, Tiggesbáumker J, Reinhard P G, Dinh P M and Suraud E 2010 Rev. Mod. Phys. 82 1793
[33] Dinh P M, Reinhard P G and Suraud E 2010 Phys. Rep. 485 43
[34] Marques M A L and Gross E K U 2004 Annu. Rev. Phys. Chem. 55 427
[35] Perdew J P and Wang Y 1992 Phys. Rev. B 45 13244
[36] Legrand C, Suraud E and Reinhard P G 2002 J. Phys. B 35 1115
[37] Goedecker S, Teter M and J Hutter 1996 Phys. Rev. B 54 1703
[38] Reinhard P G and Suraud E 2003 Introduction to Cluster Dynamics (New York: Wiley-VCH)
[39] Ullrich C A 2000 J. Mol. Struct. (THEOCHEM) 501-502 315
[40] Wang Z P, Zhang F S, Xu X F and Qian C Y 2020 Chin. Phys. B 29 023401
[41] Susi H, Ard J S and Purcell J M 1973 Spectrochimica Acta 29A 725
[42] Radchenko E D, Sheina G G, Smorygo N A and Blagoi Yu P 1984 J. Mol. Struct. 116 387
[43] Tabet J, Eden S, Feil S, Abdoul-Carime H, Farizon B, Farizon M, Ouaskit S and Märk T D 2010 Int. J. Mass Spectrom. 292 53
[44] Le Padellec A, Moretto-Capelle P, Richard-Viard M, Champeaux J P and Cafarelli P 2008 J. Phys.: Conf. Ser. 101 012007
[45] NIST Chemistry WebBook, available from
[46] Schlathölter T, Alvarado F, Bari S and Hoekstra R 2006 Phys. Scr. 73 C113
[47] Huber K P and Herzberg G 1979 Molecular Spectra and Molecular Structure IV. Constants of Diatomic Molecules (Boston: Springer)
[48] Improta R, Scalmani G and Barone V 2000 Int. J. Mass. Spectrometry 201 321
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