Citation: WU Ying-Xi, WANG Hong-Yan, LIN Yue-Xia. Aqueous Solution Effects on the Proton-Transfer Processes of GC and AT Base Pairs[J]. Acta Physico-Chimica Sinica, ;2014, 30(2): 257-264. doi: 10.3866/PKU.WHXB201312031 shu

Aqueous Solution Effects on the Proton-Transfer Processes of GC and AT Base Pairs

1.
School of Physical Science and Technology, Southwest Jiaotong University, Chengdu 610031, P. R. China

Received Date: 10 September 2013
Available Online: 3 December 2013
Fund Project: 国家自然科学基金(10974161，11174237)，国家重点基础研究发展规划项目(973)(2013CB328904) (10974161，11174237)，国家重点基础研究发展规划项目(973)(2013CB328904)四川省科技厅应用基础项目(2013JY0035)资助 (2013JY0035)

The effects of the first hydration shell and the bulk solvation effects on the proton-transfer processes of guanine-cytosine (GC) and adenine-thymine (AT) base pairs are studied based on density functional theory, using the B3LYP method and DZP++ basis set. The proton-transfer mechanisms of the GC and AT base pairs in bulk solvation are first single-proton transfer (SPT1) and stepwise double-proton transfer (DPT). When only the first hydration shell surrounded by five water molecules (GC ·5H₂O, AT· 5H₂O), or both the first hydration shell and bulk solvation effects through polarizable continuum model (PCM) (GC·5H₂O+PCM, AT·5H₂O+PCM) are considered, only the first single-proton-transfer mechanism (SPT1) is found. The proton- transfer activation energies of the GC and the AT base pairs show that the majority of the hydration effects come from the first hydration shell through hydrogen- bond interactions, therefore the first hydration shell greatly influences the base pair structures and proton-transfer mechanism.
- Density functional theory,
- Base pair,
- Proton-transfer,
- First hydration shell,
- Bulk solvation effect
1. [1]
  
  (1) Bao, X. G.;Wang, J.; Gu, J. D.; Leszczynski, J. Proc. Natl. Acad. Sci. U. S. A. 2006, 103 (15), 5658. doi: 10.1073/pnas.0510406103
2. [2]
  (2) Boudaiffa, B.; Cloutier, P.; Hunting, D.; Huels, M. A.; Sanche,L. Science 2000, 287 (5458), 1658. doi: 10.1126/science.287.5458.1658
3. [3]
  (3) Zheng, Y.; Cloutier, P.; Hunting, D. J.;Wagner, J. R.; Sanche, L.J. Am. Chem. Soc. 2004, 126 (4), 1002. doi: 10.1021/ja0388562
4. [4]
  (4) Gresh, N.; S? poner, J. J. Phys. Chem. B 1999, 103 (51), 11415.doi: 10.1021/jp9921351
5. [5]
  (5) Noguera, M.; Bertran, J.; Sodupe, M. J. Phys. Chem. B 2008,112 (15), 4817. doi: 10.1021/jp711982g
6. [6]
  (6) Tan, Z. J.; Chen, S. J. Biophys. J. 2006, 90, 1175. doi: 10.1529/biophysj.105.070904
7. [7]
  (7) Bowman, J. C.; Lenz, T. K.; Hud, N. V.;Williams, L. D. Cur. Opin. Struct. Biol. 2012, 22, 262. doi: 10.1016/j.sbi.2012.04.006
8. [8]
  (8) Zhang, Y. Theoretical Investigation of Metal Cations Interactwith DNA Base Pair. Ph. D. Dissertation, Huazhong Universityof Science and Technology,Wuhan, 2004. [张愚. 金属离子与DNA碱基对相互作用的理论研究[D]. 武汉: 华中科技大学, 2004.]
9. [9]
  (9) Shishkin, O. V.; rb, L.; Leszczynski, J. J. Phys. Chem. B2000, 104 (22), 5357. doi: 10.1021/jp993144c
10. [10]
  (10) Herbert, H. E.; Halls, M. D.; Hratchian, H. P.; Raghavachari, K.J. Phys. Chem. B 2006, 110 (7), 3336. doi: 10.1021/jp055865j
11. [11]
  (11) Matsui, T.; Shigeta, Y.; Hirao, K. Chem. Phys. Lett. 2006, 423 (4), 331.
12. [12]
  (12) Noguera, M.; Bertran, J.; Sodupe, M. J. Phys. Chem. A 2004,108 (32), 333.
13. [13]
  (13) Ai, H. Q.; Yang, A. B.; Li, Y. G. Acta Phys. -Chim. Sin. 2008,24, 1047. [艾洪奇, 杨爱彬, 李允刚. 物理化学学报, 2008,24, 1047.] doi: 10.3866/PKU.WHXB20080623
14. [14]
  (14) Zhang, F.;Wang, H. Y.; Lin, Y. X. Acta Phys. -Chim. Sin. 2011,27, 2799. [张凤, 王红艳, 林月霞. 物理化学学报, 2011, 27,2799.] doi: 10.3866/PKU.WHXB20112799
15. [15]
  (15) Löwdin, P. O. Rev. Mod. Phys. 1963, 35, 724. doi: 10.1103/RevModPhys.35.724
16. [16]
  (16) Löwdin, P. O. Adv. Quantum Chem. 1966, 2, 213.
17. [17]
  (17) Zhang, J. D.; Chen, Z. F.; Schaefer, H. F. J. Phys. Chem. A 2008,112 (27), 6217. doi: 10.1021/jp711958p
18. [18]
  (18) Kumar, A.; Sevilla, M. D.; Sándor, S. J. Phys. Chem. B 2008,112 (16), 5189. doi: 10.1021/jp710957p
19. [19]
  (19) Richardson, N. A.;Wesolowski, S. S.; Schaefer, H. F. J. Phys. Chem. B 2003, 107 (3), 848. doi: 10.1021/jp022111l
20. [20]
  (20) Xie, Y. M.; Schaefer, H. F. J. Chem. Phys. 2007, 127, 155107.doi: 10.1063/1.2780148
21. [21]
  (21) Schneider, B.; Cohen, D. M.; Schleifer, L.; Srinivasan, A. R.;Olson,W. K.; Bermant, H. M. Biophys. J. 1993, 65, 2291. doi: 10.1016/S0006-3495(93)81306-7
22. [22]
  (22) Kumar, A.; Mishra, P. C.; Suhai, S. J. Phys. Chem. A 2005, 109,3971. doi: 10.1021/jp0456178
23. [23]
  (23) Cerón-Carrasco, J. P.; Requena, A.; Michaux, C.; Perpete, E. A.;Jacquemin, D. J. Phys. Chem. A 2009, 113, 7892. doi: 10.1021/jp900782h
24. [24]
  (24) Cerón-Carrasco, J. P.; Requena, A.; Michaux, C.; Perpete, E. A.;Jacquemin, D. J. Phys. Chem. A 2009, 113, 10549. doi: 10.1021/jp906551f
25. [25]
  (25) Kumar, A.; Sevilla, M. D. J. Phys. Chem. B 2009, 113, 11359.doi: 10.1021/jp903403d
26. [26]
  (26) Chen, H. Y.; Kao, C. L.; Hsu, S. C. N. J. Am. Chem. Soc. 2009,131, 15930. doi: 10.1021/ja906899p
27. [27]
  (27) Chen, H. Y.; Hsu, S. C. N.; Kao, C. L. Phys. Chem. Chem. Phys.2010, 12, 1253. doi: 10.1039/b920603e
28. [28]
  (28) Lin, Y. X.;Wang, H. Y.; Gao, S. M.;Wu, Y. X.; Li, R. H. Acta Phys. -Chim. Sin. 2013, 29, 1233. [林月霞, 王红艳, 高思敏,吴颖曦, 李汝虎. 物理化学学报, 2013, 29, 1233.] doi: 10.3866/PKU.WHXB201304022
29. [29]
  (29) Wu, Y. X.;Wang, H. Y.; Lin, Y. X.; Gao, S. M.; Zhang, F. Can. J. Chem. 2013, 91, 992.
30. [30]
  (30) Dargiewicz, M.; Biczysko, M.; Improta, R.; Barone, V. Phys. Chem. Chem. Phys. 2012, 14, 8981. doi: 10.1039/c2cp23890j
31. [31]
  (31) Hsu, S. C. N.;Wang, T. P.; Kao, C. L.; Chen, H. F.; Yang, P. Y.;Chen, H. Y. J. Phys. Chem. B 2013, 117, 2096. doi: 10.1021/jp400299v
32. [32]
  (32) Frisch, M. J.; Trucks, G.W.; Schlegel, H. B.; et al. Gaussian 09,Revision A.1; Gaussian Inc.:Wallingford, CT, 2004.
33. [33]
  (33) Latajka, Z.; Bouteiller, Y. J. Chem. Phys. 1994, 101, 9793. doi: 10.1063/1.467944
34. [34]
  (34) Lee, C.; Fitzgerald, G.; Planas, M.; Novoa, J. J. J. Phys. Chem.1996, 100, 7398. doi: 10.1021/jp953360v
35. [35]
  (35) Huzinaga, S. J. Chem. Phys. 1965, 42, 1293. doi: 10.1063/1.1696113
36. [36]
  (36) Dunning, T. H. J. Chem. Phys. 1970, 53, 2823. doi: 10.1063/1.1674408
37. [37]
  (37) Schneider, B.; Berman, H. M. Biophys. J. 1995, 69, 2661. doi: 10.1016/S0006-3495(95)80136-0
38. [38]
  (38) Miertus, S.; Scrocco, E.; Tomasi, J. Chem. Phys. 1981, 55 (1),117. doi: 10.1016/0301-0104(81)85090-2
39. [39]
  (39) Miertus, S.; Tomasi, J. Chem. Phys. 1982, 65 (2), 239. doi: 10.1016/0301-0104(82)85072-6
40. [40]
  (40) Wang, H. Y.; Zhang, J. D.; Schaefer, H. F. Chem. Phys. Chem.2010, 11, 622. doi: 10.1002/cphc.200900687
41. [41]
  (41) Noguera, M.; Sodupe, M.; Bertrán, J. Theor. Chem. Acc. 2007,118, 113. doi: 10.1007/s00214-007-0248-z
42. [42]
  (42) Florián, J.; LeszczyDski, J. J. Am. Chem. Soc. 1996, 118, 3010.doi: 10.1021/ja951983g
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]
  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
4. [4]
  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
5. [5]
  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): 100012-. doi: 10.3866/PKU.WHXB202309027
6. [6]
  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
7. [7]
  Xiaochen Zhang , Fei Yu , Jie Ma . 多角度数理模拟在电容去离子中的前沿应用. Acta Physico-Chimica Sinica, 2024, 40(11): 2311026-. doi: 10.3866/PKU.WHXB202311026
8. [8]
  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
9. [9]
  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
10. [10]
  Yaping Li , Sai An , Aiqing Cao , Shilong Li , Ming Lei . The Application of Molecular Simulation Software in Structural Chemistry Education: First-Principles Calculation of NiFe Layered Double Hydroxide. University Chemistry, 2025, 40(3): 160-170. doi: 10.12461/PKU.DXHX202405185
11. [11]
  Xin XIONG , Qian CHEN , Quan XIE . First principles study of the photoelectric properties and magnetism of La and Yb doped AlN. Chinese Journal of Inorganic Chemistry, 2024, 40(8): 1519-1527. doi: 10.11862/CJIC.20240064
12. [12]
  Lina Guo , Ruizhe Li , Chuang Sun , Xiaoli Luo , Yiqiu Shi , Hong Yuan , Shuxin Ouyang , Tierui Zhang . 层状双金属氢氧化物的层间阴离子对衍生的Ni-Al₂O₃催化剂光热催化CO₂甲烷化反应的影响. Acta Physico-Chimica Sinica, 2025, 41(1): 2309002-. doi: 10.3866/PKU.WHXB202309002
13. [13]
  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
14. [14]
  Lu XU , Chengyu ZHANG , Wenjuan JI , Haiying YANG , Yunlong FU . Zinc metal-organic framework with high-density free carboxyl oxygen functionalized pore walls for targeted electrochemical sensing of paracetamol. Chinese Journal of Inorganic Chemistry, 2024, 40(5): 907-918. doi: 10.11862/CJIC.20230431
15. [15]
  Jin CHANG . Supercapacitor performance and first-principles calculation study of Co-doping Ni(OH)₂. Chinese Journal of Inorganic Chemistry, 2024, 40(9): 1697-1707. doi: 10.11862/CJIC.20240108
16. [16]
  Qiuyang LUO , Xiaoning TANG , Shu XIA , Junnan LIU , Xingfu YANG , Jie LEI . Application of a densely hydrophobic copper metal layer in-situ prepared with organic solvents for protecting zinc anodes. Chinese Journal of Inorganic Chemistry, 2024, 40(7): 1243-1253. doi: 10.11862/CJIC.20240110
17. [17]
  Zhenming Xu , Mingbo Zheng , Zhenhui Liu , Duo Chen , Qingsheng Liu . Experimental Design of Project-Driven Teaching in Computational Materials Science: First-Principles Calculations of the LiFePO₄ Cathode Material for Lithium-Ion Batteries. University Chemistry, 2024, 39(4): 140-148. doi: 10.3866/PKU.DXHX202307022
18. [18]
  Xiaojun Wu , Kai Hu , Faqiong Zhao . Laying the Groundwork for General Chemistry Experiment Teaching: Exploration and Summary of Assisting Experiment Preparatory Work through Online and Offline Integration. University Chemistry, 2024, 39(8): 23-27. doi: 10.3866/PKU.DXHX202312052
19. [19]
  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
20. [20]
  Xinyu ZENG , Guhua TANG , Jianming OUYANG . Inhibitory effect of Desmodium styracifolium polysaccharides with different content of carboxyl groups on the growth, aggregation and cell adhesion of calcium oxalate crystals. Chinese Journal of Inorganic Chemistry, 2024, 40(8): 1563-1576. doi: 10.11862/CJIC.20230374

Get Citation

PDF

XML

Metrics

PDF Downloads(442)
Abstract views(751)
HTML views(4)

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