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Chin. Phys. B, 2014, Vol. 23(2): 027103    DOI: 10.1088/1674-1056/23/2/027103
CONDENSED MATTER: ELECTRONIC STRUCTURE, ELECTRICAL, MAGNETIC, AND OPTICAL PROPERTIES Prev   Next  

Damage mechanism of hydroxyl radicals toward adenine–thymine base pair

Tan Rong-Ria b c, Wang Dong-Qie, Zhang Feng-Shoub d f
a College of Communication and Electronics, Jiangxi Science & Technology Normal University, Nanchang 330013, China;
b The Key Laboratory of Beam Technology and Material Modification of the Ministry of Education, College of Nuclear Science and Technology, Beijing Normal University, Beijing 100875, China;
c Guizhou Key Laboratory for Photoelectric and Application, College of Science, Guizhou University, Guiyang 550025, China;
d Beijing Radiation Center, Beijing 100875, China;
e Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China;
f Center of Theoretical Nuclear Physics, National Laboratory of the Heavy Ion Accelerator of Lanzhou, Lanzhou 730000, China
Abstract  The adenine–thymine base pair was studied in the presence of hydroxyl radicals in order to probe the hydrogen bond effect. The results show that the hydrogen bonds have little effect on the hydroxylation and dehydrogenation happened at the sites, which are not involved in a hydrogen bond, while at the sites involved in hydrogen bond formation in the base pair, the reaction becomes more difficult, both in view of the free energy barrier and the exothermicity. With a 6-311++G(d,p) level of description, both B3LYP and MP2 methods confirm that the C8 site of isolated adenine has the highest possibility to form covalent bond with the hydroxyl radicals, though with different energetics: B3LYP predicts a barrierless pathway, while MP2 finds a transition state with an energy of 106.1 kJ/mol. For the dehydrogenation reactions, B3LYP method predicts that the free energy barrier increases in the order of HN9 < HN61 < HN62 < H2 < H8.
Keywords:  DNA damage      hydrogen bond effect      hydroxylation      dehydrogenation     
Received:  19 October 2013      Published:  12 December 2013
PACS:  71.15.Mb (Density functional theory, local density approximation, gradient and other corrections)  
  82.30.Cf (Atom and radical reactions; chain reactions; molecule-molecule reactions)  
  82.39.Pj (Nucleic acids, DNA and RNA bases?)  
  87.15.Fh (Bonding; mechanisms of bond breakage)  
Fund: Project supported by the National Natural Science Foundation of China (Grant Nos. 11025524 and 11161130520), the National Basic Research Program of China (Grant No. 2010CB832903), the Natural Science Foundation of Guizhou Province of China (Grant No. J20122141), the Fund in the framework of a Frontier of Novelty Program of the Chinese Academy of Sciences for one of the authors (Wang Dong-Qi) (Grant No. Y1515540U1), and the Research Fund for the Doctoral Program of Jiangxi Science and Technology Normal University (Grant No. 3000990110).
Corresponding Authors:  Wang Dong-Qi, Zhang Feng-Shou     E-mail:  dwang@ihep.ac.cn;fszhang@bnu.edu.cn
About author:  71.15.Mb; 82.30.Cf; 82.39.Pj; 87.15.Fh

Cite this article: 

Tan Rong-Ri, Wang Dong-Qi, Zhang Feng-Shou Damage mechanism of hydroxyl radicals toward adenine–thymine base pair 2014 Chin. Phys. B 23 027103

[1] Steenken S 1989 Chem. Rev. 89 503
[2] D’Souza J S, Dharmadhikari J A, Dharmadhikari A K, Rao B J, Mathur D 2011 Phys. Rev. Lett. 106 118101
[3] 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
[4] Becker D, Adhikary A, Sevilla M and Chakraborty T 2007 Charge Migration in DNA: Physics, Chemistry and Biology Perspectives (New York: Springer)
[5] Wu Y, Mundy C J, Colvin M E and Car R 2004 J. Phys. Chem. A 108 2922
[6] Schyman P, Eriksson L A, Zhang R B and Laaksonen A 2008 Chem. Phys. Lett. 458 186
[7] Xia J F and Jia Y 2010 Chin. Phys. B 19 040506
[8] Wetmore S D, Boyd R J and Eriksson L A 1998 J. Phys. Chem. B 102 5369
[9] Grand A, Morell C, Labet V, Cadet J and Eriksson L A 2007 J. Phys. Chem. A 111 8968
[10] Agnihotri N and Mishra P 2011 Chem. Phys. Lett. 503 305
[11] Qi W P and Lei X L 2011 Chin. Phys. Lett. 28 048702
[12] Cadet J, Douki T and Ravanat J L 2010 Free Radic. Biol. Med. 49 9
[13] Kumar A, Pottiboyina V and Sevilla M D 2011 J. Phys. Chem. B 115 15129
[14] Abolfath R M, Biswas P K, Rajnarayanam R, Brabec T, Kodym R and Papiez L 2012 J. Phys. Chem. A 116 3940
[15] Shintaro F and Yu Y X 2010 Chin. Phys. B 19 088701
[16] Kravec S M, Kinz-Thompson C D and Conwell E M 2011 J. Phys. Chem. B 115 6166
[17] von Sonntag C 2006 Free-Radical-Induced DNA Damage and Its Repair: a Chemical Perspective (Berlin: Springer-Verlag)
[18] Cadet J, Delatour T, Douki T, Gasparutto D, Pouget J P, Ravanat J L and Sauvaigo S 1999 Mutat. Res. Fundam. Mol. Mech. Mutagen. 424 9
[19] Candeias L P and Steenken S 2000 Chem. Eur. J. 6 475
[20] Chatgilialoglu C, D’Angelantonio M, Guerra M, Kaloudis P and Mulazzani Q 2009 Angew. Chem. Int. Ed. 48 2214
[21] Phadatare S D, Sharma K K K, Rao B S M, Naumov S and Sharma G K 2011 J. Phys. Chem. B 115 13650
[22] Su X, Huang Q, Dang B, Wang X and Yu Z 2011 Radiat. Phys. Chem. 80 1343
[23] Cheng Q, Gu J, Compaan K R and Schaefer H F 2010 Chem. Eur. J. 16 11848
[24] Aydogan B, Bolch W E, Swarts S G, Turner J E and Marshall D T 2008 Radiat. Res. 169 223
[25] Mundy C J, Colvin M E and Quong A A 2002 J. Phys. Chem. A 106 10063
[26] Vieira A J S C, Steenken S 1990 J. Am. Chem. Soc. 112 6986
[27] Llano J and Eriksson L A 2004 Phys. Chem. Chem. Phys. 6 4707
[28] Naumov S and von Sonntag C 2008 Radiat. Res. 169 355
[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] Guerra C F, van der Wijst T, Poater J, Swart M and Bickelhaupt F M 2010 Theor. Chem. Acc. 125 245
[32] Lee C, Yang W and Parr R G 1988 Phys. Rev. B 37 785
[33] Becke A D 1993 J. Chem. Phys. 98 5648
[34] Wang F, Zhang F S and Eric S 2003 Chin. Phys. 12 164
[35] Wei H Y, Xiong X L, Song H T and Luo S Z 2010 Chin. Phys. Lett. 27 097102
[36] Moller C, Plesset M S 1934 Phys. Rev. 46 618
[37] Frisch M J, Head-Gordon M and Pople J A 1990 Chem. Phys. Lett. 166 275
[38] Tan R R, Wang D Q, Hu L and Zhang F S 2013 Int. J. Quantun Chem. DOI: 10.1002/qua.24567
[39] Frisch M J, Pople J A and Binkley J S 1984 J. Chem. Phys. 80 3265
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