Computational mechanistic investigation of radiation damage of adenine induced by hydroxyl radicals

doi:10.1088/1674-1056/27/2/027102

Abstract The radiation damage of adenine base was studied by B3LYP and MP2 methods in the presence of hydroxyl radicals to probe the reactivities of five possible sites of an isolated adenine molecule. Both methods predict that the C8 site is the more vulnerable than the other sites. For its bonding covalently with the hydroxyl radicals, B3LYP predicts a barrierless pathway, while MP2 finds a transition state with an energy of 106.1 kJ/mol. For the hydroxylation at the C2 site, the barrier was calculated to be 165.3 kJ/mol using MP2 method. For the dehydrogenation reactions at five sites of adenine, B3LYP method predicts that the free energy barrier decreases in the order of H8 > H2 > HN62 > HN61 > HN9.

Keywords: DNA damage radicals adenine dehydrogenation

Received: 30 August 2017
Revised: 01 December 2017
Accepted manuscript online:

PACS:	71.15.Mb	(Density functional theory, local density approximation, gradient and other corrections)
	82.20.Kh	(Potential energy surfaces for chemical reactions)
	82.39.-k	(Chemical kinetics in biological systems)
	87.15.Fh	(Bonding; mechanisms of bond breakage)

Fund: Project supported by the National Natural Science Foundation of China (Grant Nos. 11564015 and 61404062), the Research Fund for the Doctoral Program of China (Grant No. 3000990110), and the Fund for Distinguished Young Scholars of Jiangxi Science & Technology Normal University (Grant Nos. 2015QNBJRC002 and 2016QNBJRC006).

Corresponding Authors: Rongri Tan
E-mail: rrtan@163.com

About author: 71.15.Mb; 82.20.Kh; 82.39.-k; 87.15.Fh

Cite this article:

Rongri Tan(谈荣日), Huixuan Liu(刘慧宣), Damao Xun(寻大毛), Wenjun Zong(宗文军) Computational mechanistic investigation of radiation damage of adenine induced by hydroxyl radicals 2018 Chin. Phys. B 27 027102

[1]	Pouget J P, Frelon S, Ravanat J L, Testard I, Odin F and Cadet J 2002 Radiat. Res. 157 589
[2]	Cadet J, Sage E and Douki T 2005 Mutat. Res. 571 3
[3]	Steenken S 1989 Chem. Rev. 89 503
[4]	D'Souza J S, Dharmadhikari J A, Dharmadhikari A K, Rao B J and Mathur D 2011 Phys. Rev. Lett. 106 118101
[5]	Mauceri H J, Hanna N N, Beckett M A, Gorski D H, Staba M J, Stellato K A, Bigelow K, Heimann R, Gately S, Dhanabal M, Soff G A, Sukhatme V P, Kufe D W and Weichselbaum R R 1998 Nature 394 287
[6]	Becker D, Adhikary A, Sevilla M and Chakraborty T 2007 Charge Migration in DNA:Physics, Chemistry and Biology Perspectives (New York:Springer)
[7]	Wu Y, Mundy C J, Colvin M E and Car R 2004 J. Phys. Chem. A 108 2922
[8]	Schyman P, Eriksson L A, Zhang R B and Laaksonen A 2008 Chem. Phys. Lett. 458 186
[9]	Xia J F and Jia Y 2010 Chin. Phys. B 19 040506
[10]	Wetmore S D, Boyd R J and Eriksson L A 1998 J. Phys. Chem. B 102 5369
[11]	Grand A, Morell C, Labet V, Cadet J and Eriksson L A 2007 J. Phys. Chem. A 111 8968
[12]	Agnihotri N and Mishra P 2011 Chem. Phys. Lett. 503 305
[13]	Cadet J, Douki T and Ravanat J L 2010 Free Radic. Biol. Med. 49 9
[14]	Kumar A, Pottiboyina V and Sevilla M D 2011 J. Phys. Chem. B 115 15129
[15]	Abolfath R M, Biswas P K, Rajnarayanam R, Brabec T, Kodym R and Papiez L 2012 J. Phys. Chem. A 116 3940
[16]	Shintaro F and Yu Y X 2010 Chin. Phys. B 19 088701
[17]	Kravec S M, Kinz-Thompson C D and Conwell E M 2011 J. Phys. Chem. B 115 6166
[18]	von Sonntag C 2006 Free-radical-induced DNA damage and its repair:a chemical perspective (Berlin:Springer Verlag)
[19]	Cadet J, Delatour T, Douki T, Gasparutto D, Pouget J P, Ravanat J L and Sauvaigo S 2011 Mutat. Res./Fundam. Mol. Mech. Mutagen. 424 9
[20]	Candeias L P and Steenken S 2000 Chem. Eur. J. 6 475
[21]	Chatgilialoglu C, D'Angelantonio M, Guerra M, Kaloudis P and Mulazzani Q 2009 Angew. Chem. Int. Ed. 48 2214
[22]	Davis J T 2004 Angew. Chem. Int. Ed. 43 668.
[23]	Su X, Huang Q, Dang B, Wang X and Yu Z 2011 Radiat. Phys. Chem. 80 1343.
[24]	Patel P K, Koti A S R and Hosur R V 1999 Nucleic Acid Res. 27 3836
[25]	Cheng Q Y, Gu J D, Compaan K R and Schaefer Ⅲ H F 2010 Chem. Eur. 16 11848
[26]	Aydogan B, Bolch W E, Swarts S G, Turner J E and Marshall D T 2008 Radiat. Res. 169 223.
[27]	Mundy C J, Colvin M E and Quong A A 2002 J. Phys. Chem. A 106 10063
[28]	Tan R R, Wang D Q, Hu L and Zhang F S 2014 Int. J. Quantum Chem. 114 367
[29]	Gu J, Xie Y and Schaefer H F 2006 J. Phys. Chem. B 110 19696
[30]	Yamagami R, Kobayashi K and Tagawa S 2008 J. Am. Chem. Soc. 130 14772
[31]	Tan R R, Wang D Q, Hu L and Zhang F S 2014 Chin. Phys. B 23 027103
[32]	Guerra C F, van der Wijst T, Poater J, Swart M and Bickelhaupt F M 2010 Theor. Chem. Acc. 125 245
[33]	Naumov S and von Sonntag C 2008 Radiat. Res. 169 355
[34]	Llano J and Eriksson L A 2004 Phys. Chem. Chem. Phys. 6 4707
[35]	Vieira A J S C and Steennken S 1990 J. Am. Chem. Soc. 112 6986
[36]	Lee C, Yang W and Parr R G 1988 Phys. Rev. B 37 785
[37]	Becke A D 1993 J. Chem. Phys. 98 5648
[38]	Møller C and Plesset M S 1934 Phys. Rev. 46 618
[39]	Frisch M J, Head-Gordon M and Pople J A 1990 Chem. Phys. Lett. 166 275
[40]	Frisch M J, Pople J A and Binkley J S 1984 J. Chem. Phys. 80 3265
[41]	Clark T, Chandrasekhar J, Spitznagel G W and Schleyer P von R 1983 J. Comput. Chem. 4 294
[42]	Grimme S 2006 J. Comput. Chem. 27 1787.
[43]	Llano J 2004 Modern Computational Physical Chemistry:An Introduction to Biomolecular Radiation Damage and Photoxicity (Comprehensive Summaries of Uppsala Dissertation from the Faculty of Science and Technology 965, Acta Universiatis Upsaliensis, Uppsala)

[1]	Synthesis of hexagonal boron nitride films by dual temperature zone low-pressure chemical vapor deposition Zhi-Fu Zhu(朱志甫), Shao-Tang Wang(王少堂), Ji-Jun Zou(邹继军), He Huang(黄河), Zhi-Jia Sun(孙志嘉), Qing-Lei Xiu(修青磊), Zhong-Ming Zhang(张忠铭), Xiu-Ping Yue(岳秀萍), Yang Zhang(张洋), Jin-Hui Qu(瞿金辉), and Yong Gan(甘勇). Chin. Phys. B, 2022, 31(8): 086103.
[2]	Thermo-controllable self-assembled structures of single-layer 4, 4"-diamino-p-terphenyl molecules on Au (110) Junhai Ren(任俊海), Deliang Bao(包德亮), Li Dong(董立), Lei Gao(高蕾), Rongting Wu(武荣庭), Linghao Yan(闫凌昊), Aiwei Wang(王爱伟), Jiahao Yan(严佳浩), Yeliang Wang(王业亮), Shixuan Du(杜世萱), Qing Huan(郇庆), Hongjun Gao(高鸿钧). Chin. Phys. B, 2017, 26(8): 086801.
[3]	LIF diagnostics of hydroxyl radical in a methanol containing atmospheric-pressure plasma jet Mu-Yang Qian(钱沐杨), San-Qiu Liu(刘三秋), Xue-Kai Pei(裴学凯), Xin-Pei Lu(卢新培), Jia-Liang Zhang(张家良), De-Zhen Wang(王德真). Chin. Phys. B, 2016, 25(10): 105205.
[4]	Numerical study of the effect of water content on OH production in a pulsed-dc atmospheric pressure helium-air plasma jet Mu-Yang Qian(钱沐杨), Cong-Ying Yang(杨从影), Zhen-dong Wang(王震东), Xiao-Chang Chen(陈小昌), San-Qiu Liu(刘三秋), De-Zhen Wang(王德真). Chin. Phys. B, 2016, 25(1): 015202.
[5]	Damage mechanism of hydroxyl radicals toward adenine–thymine base pair Tan Rong-Ri (谈荣日), Wang Dong-Qi (王东琪), Zhang Feng-Shou (张丰收). Chin. Phys. B, 2014, 23(2): 027103.
[6]	Radiation-induced robust oscillation and non-Gaussian fluctuation Liu Bo(刘波), Yan Shi-Wei (晏世伟), and Geng Yi-Zhao(耿轶钊) . Chin. Phys. B, 2011, 20(12): 128702.
[7]	A mathematical model of a P53 oscillation network triggered by DNA damage Xia Jun-Feng(夏俊峰) and Jia Ya(贾亚) . Chin. Phys. B, 2010, 19(4): 040506.
[8]	Spatial distribution of SiCl_n (n=0--2) in SiCl₄ plasma measured by mass spectroscopy Wang Zhao-Kui(王照奎), Lin Kui-Xun(林揆训), Lou Yan-Hui(娄艳辉), Lin Xuan-Ying(林璇英), and Zhu Zu-Song(祝祖送). Chin. Phys. B, 2006, 15(10): 2374-2377.
[9]	Study of effect of H₂ addition on the production of fluorocarbon radicals in H₂C₄F₈ inductively coupled plasma via optical emission spectroscopy actinometry Huang Song (黄松), Xin Yu (辛煜), Ning Zhao-Yuan (宁兆元). Chin. Phys. B, 2005, 14(8): 1608-1612.
[10]	ESR of dislocation defects in MgF₂ crystals－with more than 130 line peaks Hou Bi-Hui (侯碧辉), Zheng Ying-Guang (郑莹光), Shao Meng (邵萌), Liu Feng-Yan (刘凤艳), Fan Zhi-Da (范志达). Chin. Phys. B, 2005, 14(7): 1453-1456.

No Suggested Reading articles found!

Viewed

Full text

Abstract

Cited

Metrics
Related Articles

Computational mechanistic investigation of radiation damage of adenine induced by hydroxyl radicals

Cite this article:

Online attention