Citation: SHI Jun-You, DONG Li-Hua, LIU Yong-Jun. Effect of Hydroxylation on Structures and Proton Transfer of A-T Base Pairs[J]. Acta Physico-Chimica Sinica, ;2010, 26(12): 3329-3336. doi: 10.3866/PKU.WHXB20101136 shu

Effect of Hydroxylation on Structures and Proton Transfer of A-T Base Pairs

1.
1. Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810001, P. R. China;
2. Graduate University of Chinese Academy of Sciences, Beijing 100049, P. R. China

Received Date: 2 August 2010
Available Online: 18 October 2010
Fund Project:

The structures and proton transfer processes of hydroxylated A-T base pairs were theoretically studied at the B3LYP/6-31++G(d,p)//B3LYP/6-31G(d,p) level. Our calculations revealed that hydroxyl radical could react with A-T at different positions to form eight stable adducts. The order of these adducts in energy is ^8OHA-T<A-T^6OH<A-T^5OH<^2OHA-T<^4OHA-T<^5OHA-T<A-T^2OH<A-T^4OH (the number denotes the label of the atom in the A/T which is attacked by hydroxyl), which relates well with their structural changes upon the addition of hydroxyl radical. The interaction energy between A and T would increase slightly when hydroxyl radical reacts with the adenine, but it would decrease when the radical reacts with thymine. To study the proton transfer processes of the hydroxylated A-T base pairs, the most stable adducts, ^8OHA-T and A-T6OH, were selected to give calculations. The calculated results indicate that the proton transfer processes of ^8OHA-T and A-T^6OH follow the concerted mechanism, which is different from the stepwise mechanism of A-T. What is more, its energy barrier is lower than the corresponding energy of the latter's first step (rate-determining step).
- Density functional theory,
- Base pair,
- Hydroxylation,
- Proton transfer,
- Singly occupied molecular orbital
1. [1]
  
  1. Breen, A. P.; Murphy, J. A. Free Radical Bio. Med., 1995, 18: 1033
2. [2]
  2. Burrows, C. J.; Muller, J. G. Chem. Rev., 1998, 98: 1109
3. [3]
  3. Steenken, S.; Novais, H. M. J. Phys. Chem., 1987, 91: 426
4. [4]
  4. Vieira, A. J. S. C.; Steenken, S. J. Am. Chem. Soc., 1990, 112: 6986
5. [5]
  5. Steenken, S. Chem. Rev., 1989, 89: 503
6. [6]
  6. Colson, A. O.; Sevilla, M. D. J. Phys. Chem., 1996, 100: 4420
7. [7]
  7. Lowdin, P. O. Adv. Quantum Chem., 1965, 2: 213
8. [8]
  8. Piccirilli, J. A.; Krauch, T.; Moroney, S. E.; Benner, S. A. Nature, 1990, 343: 33
9. [9]
  9. Benderskii, V. A.; Makarov, D. E.;Wight, C. A. Chemical dynamic at low temperature: advances in chemical physics. New York:Wiley& Sons, 1994
10. [10]
  10. Zhanpeisov, N. U., Leszczynski, J. J. Phys. Chem. A, 1998, 102: 6167
11. [11]
  11. Truhlar, D. G. Chem. Phys. Lett., 1998, 294: 45
12. [12]
  12. Floribn, J.; Hrouda, V.; Pave1, H. J. Am. Chem. Soc., 1994, 116: 1457
13. [13]
  13. rb, L.; Podolyan, Y.; Dziekonski, P.; Sokalski, A.; Leszczynski, J. J. Am. Chem. Soc., 2004, 126: 10119
14. [14]
  14. Kryachk, E. S.; Sabin, J. R. Int. J. Quantum Chem., 2003, 91: 695
15. [15]
  15. Villani, G. Chem. Phys., 2005, 316: 1
16. [16]
  16. Xie, H.; Xia, F.; Cao, Z. J. Phys. Chem. A, 2007, 111: 4384
17. [17]
  17. Zhang, J. D.; Schaefee III, H. F. J. Chem. Theory Comput., 2007, 3: 115
18. [18]
  18. Grand, A.; Morell, C.; Labet, V.; Cadet, J.; Eriksson, L. A. J. Phys. Chem. A, 2007, 111: 8968
19. [19]
  19. Li, L.;Wang, H.; Niu, X. J.; Li, Z. H. Chem. J. Chin. Univ., 2009, 30: 1596
20. [20]
  [李澜, 王竑, 牛晓娟, 李宗和. 高等学校化学学报, 2009, 30: 1596]
21. [21]
  20. Zhang, R. B.; Eriksson, L. A. J. Phys. Chem. B, 2007, 111: 6571
22. [22]
  21. Hohenberg, P.; Kohn,W. Phys. Rev. B, 1964, 136: 864
23. [23]
  22. Feller, D. J. Chem. Phys., 1990, 93: 579
24. [24]
  23. Lee, C.; Yang,W.; Parr, R. G. Phys. Rev. B, 1988, 37: 785
25. [25]
  24. Becke, A. D. J. Chem. Phys., 1993, 98: 5648
26. [26]
  25. Frisch, M. J.; Trucks, G.W.; Schlegel, H. B.; et al. Gaussian 03. Revision B.03. Pittsburgh, PA: Gaussian Inc., 2003
27. [27]
  26. Hammond, G. S. J. Am. Chem. Soc., 1955, 77: 334
1. [1]
  Hao XU , Ruopeng LI , Peixia YANG , Anmin LIU , Jie BAI . Regulation mechanism of halogen axial coordination atoms on the oxygen reduction activity of Fe-N₄ site: A density functional theory study. Chinese Journal of Inorganic Chemistry, 2025, 41(4): 695-701. doi: 10.11862/CJIC.20240302
2. [2]
  Jie ZHAO , Sen LIU , Qikang YIN , Xiaoqing LU , Zhaojie WANG . Theoretical calculation of selective adsorption and separation of CO₂ by alkali metal modified naphthalene/naphthalenediyne. Chinese Journal of Inorganic Chemistry, 2024, 40(3): 515-522. doi: 10.11862/CJIC.20230385
3. [3]
  Yanglin Jiang , Mingqing Chen , Min Liang , Yige Yao , Yan Zhang , Peng Wang , Jianping Zhang . Experimental and Theoretical Investigations of Solvent Polarity Effect on ESIPT Mechanism in 4′-N,N-diethylamino-3-hydroxybenzoflavone. Acta Physico-Chimica Sinica, 2025, 41(2): 2309027-0. doi: 10.3866/PKU.WHXB202309027
4. [4]
  Meifeng Zhu , Jin Cheng , Kai Huang , Cheng Lian , Shouhong Xu , Honglai Liu . Classical Density Functional Theory for Understanding Electrochemical Interface. University Chemistry, 2025, 40(3): 148-152. doi: 10.12461/PKU.DXHX202405166
5. [5]
  Kaifu Zhang , Shan Gao , Bin Yang . Application of Theoretical Calculation with Fun Practice in Raman Spectroscopy Experimental Teaching. University Chemistry, 2025, 40(3): 62-67. doi: 10.12461/PKU.DXHX202404045
6. [6]
  Jie ZHAO , Huili ZHANG , Xiaoqing LU , Zhaojie WANG . Theoretical calculations of CO₂ capture and separation by functional groups modified 2D covalent organic framework. Chinese Journal of Inorganic Chemistry, 2025, 41(2): 275-283. doi: 10.11862/CJIC.20240213
7. [7]
  Yupeng TANG , Haiying YANG , Fan JIN , Nan LI . Hydrogen storage properties of C₆S₆Li₆: A density functional theory study. Chinese Journal of Inorganic Chemistry, 2025, 41(9): 1827-1839. doi: 10.11862/CJIC.20240460
8. [8]
  Maitri Bhattacharjee , Rekha Boruah Smriti , R. N. Dutta Purkayastha , Waldemar Maniukiewicz , Shubhamoy Chowdhury , Debasish Maiti , Tamanna Akhtar . Synthesis, structural characterization, bio-activity, and density functional theory calculation on Cu(Ⅱ) complexes with hydrazone-based Schiff base ligands. Chinese Journal of Inorganic Chemistry, 2024, 40(7): 1409-1422. doi: 10.11862/CJIC.20240007
9. [9]
  Weina Wang , Lixia Feng , Fengyi Liu , Wenliang Wang . Computational Chemistry Experiments in Facilitating the Study of Organic Reaction Mechanism: A Case Study of Electrophilic Addition of HCl to Asymmetric Alkenes. University Chemistry, 2025, 40(3): 206-214. doi: 10.12461/PKU.DXHX202407022
10. [10]
  Zhengkun QIN , Zicong PAN , Hui TIAN , Wanyi ZHANG , Mingxing SONG . A series of iridium(Ⅲ) complexes with fluorophenyl isoquinoline ligand and low-efficiency roll-off properties: A density functional theory study. Chinese Journal of Inorganic Chemistry, 2025, 41(6): 1235-1244. doi: 10.11862/CJIC.20240429
11. [11]
  Tongqi Ye , Yanqing Wang , Qi Wang , Huaiping Cong , Xianghua Kong , Yuewen Ye . Reform of Classical Thermodynamics Curriculum from the Perspective of Computational Chemistry. University Chemistry, 2025, 40(7): 387-392. doi: 10.12461/PKU.DXHX202409128
12. [12]
  Wei Sun , Yongjing Wang , Kun Xiang , Saishuai Bai , Haitao Wang , Jing Zou , Arramel , Jizhou Jiang . CoP Decorated on Ti₃C₂T_x MXene Nanocomposites as Robust Electrocatalyst for Hydrogen Evolution Reaction. Acta Physico-Chimica Sinica, 2024, 40(8): 2308015-0. doi: 10.3866/PKU.WHXB202308015
13. [13]
  Xiaochen Zhang , Fei Yu , Jie Ma . Cutting-Edge Applications of Multi-Angle Numerical Simulations for Capacitive Deionization. Acta Physico-Chimica Sinica, 2024, 40(11): 2311026-0. doi: 10.3866/PKU.WHXB202311026
14. [14]
  Lihui Jiang , Wanrong Dong , Hua Yang , Yongqing Xia , Hongjian Peng , Jun Yuan , Xiaoqian Hu , Zihan Zeng , Yingping Zou , Yiming Luo . Study on Extraction of p-Hydroxyacetophenone. University Chemistry, 2024, 39(11): 259-268. doi: 10.12461/PKU.DXHX202402056
15. [15]
  Guangming YIN , Huaiyao WANG , Jianhua ZHENG , Xinyue DONG , Jian LI , Yi'nan SUN , Yiming GAO , Bingbing WANG . Preparation and photocatalytic degradation performance of Ag/protonated g-C₃N₄ nanorod materials. Chinese Journal of Inorganic Chemistry, 2024, 40(8): 1491-1500. doi: 10.11862/CJIC.20240086
16. [16]
  Yongqing Kuang , Jie Liu , Jianjun Feng , Wen Yang , Shuanglian Cai , Ling Shi . Experimental Design for the Two-Step Synthesis of Paracetamol from 4-Hydroxyacetophenone. University Chemistry, 2024, 39(8): 331-337. doi: 10.12461/PKU.DXHX202403012
17. [17]
  Tao Cao , Fang Fang , Nianguang Li , Yinan Zhang , Qichen Zhan . Green Synthesis of p-Hydroxybenzonitrile Catalyzed by Spinach Extracts under Red-Light Irradiation: Research and Exploration of Innovative Experiments for Pharmacy Undergraduates. University Chemistry, 2024, 39(5): 63-69. doi: 10.3866/PKU.DXHX202309098
18. [18]
  Jinyao Du , Xingchao Zang , Ningning Xu , Yongjun Liu , Weisi Guo . Electrochemical Thiocyanation of 4-Bromoethylbenzene. University Chemistry, 2024, 39(6): 312-317. doi: 10.3866/PKU.DXHX202310039
19. [19]
  Xuefei Zhao , Xuhong Hu , Zhenhua Jia . 理论与计算化学在傅-克烷基化反应教学中的应用. University Chemistry, 2025, 40(8): 360-367. doi: 10.12461/PKU.DXHX202410008
20. [20]
  Xiaofang Li , Zhigang Wang . 调节金助催化剂的d_z²占据轨道增强光催化合成H₂O₂. Acta Physico-Chimica Sinica, 2025, 41(7): 100080-0. doi: 10.1016/j.actphy.2025.100080

Get Citation

PDF

XML

Metrics

PDF Downloads(1193)
Abstract views(3266)
HTML views(51)

通讯作者: 陈斌, bchen63@163.com

1.
沈阳化工大学材料科学与工程学院沈阳 110142