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
-
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.
-
-
-
[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) 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) 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) Gresh, N.; S? poner, J. J. Phys. Chem. B 1999, 103 (51), 11415.doi: 10.1021/jp9921351
-
[5]
(5) Noguera, M.; Bertran, J.; Sodupe, M. J. Phys. Chem. B 2008,112 (15), 4817. doi: 10.1021/jp711982g
-
[6]
(6) Tan, Z. J.; Chen, S. J. Biophys. J. 2006, 90, 1175. doi: 10.1529/biophysj.105.070904
-
[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) 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) Shishkin, O. V.; rb, L.; Leszczynski, J. J. Phys. Chem. B2000, 104 (22), 5357. doi: 10.1021/jp993144c
-
[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) Matsui, T.; Shigeta, Y.; Hirao, K. Chem. Phys. Lett. 2006, 423 (4), 331.
-
[12]
(12) Noguera, M.; Bertran, J.; Sodupe, M. J. Phys. Chem. A 2004,108 (32), 333.
-
[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) 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) Löwdin, P. O. Rev. Mod. Phys. 1963, 35, 724. doi: 10.1103/RevModPhys.35.724
-
[16]
(16) Löwdin, P. O. Adv. Quantum Chem. 1966, 2, 213.
-
[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) Kumar, A.; Sevilla, M. D.; Sándor, S. J. Phys. Chem. B 2008,112 (16), 5189. doi: 10.1021/jp710957p
-
[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) Xie, Y. M.; Schaefer, H. F. J. Chem. Phys. 2007, 127, 155107.doi: 10.1063/1.2780148
-
[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) Kumar, A.; Mishra, P. C.; Suhai, S. J. Phys. Chem. A 2005, 109,3971. doi: 10.1021/jp0456178
-
[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) 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) Kumar, A.; Sevilla, M. D. J. Phys. Chem. B 2009, 113, 11359.doi: 10.1021/jp903403d
-
[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) Chen, H. Y.; Hsu, S. C. N.; Kao, C. L. Phys. Chem. Chem. Phys.2010, 12, 1253. doi: 10.1039/b920603e
-
[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) Wu, Y. X.;Wang, H. Y.; Lin, Y. X.; Gao, S. M.; Zhang, F. Can. J. Chem. 2013, 91, 992.
-
[30]
(30) Dargiewicz, M.; Biczysko, M.; Improta, R.; Barone, V. Phys. Chem. Chem. Phys. 2012, 14, 8981. doi: 10.1039/c2cp23890j
-
[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) Frisch, M. J.; Trucks, G.W.; Schlegel, H. B.; et al. Gaussian 09,Revision A.1; Gaussian Inc.:Wallingford, CT, 2004.
-
[33]
(33) Latajka, Z.; Bouteiller, Y. J. Chem. Phys. 1994, 101, 9793. doi: 10.1063/1.467944
-
[34]
(34) Lee, C.; Fitzgerald, G.; Planas, M.; Novoa, J. J. J. Phys. Chem.1996, 100, 7398. doi: 10.1021/jp953360v
-
[35]
(35) Huzinaga, S. J. Chem. Phys. 1965, 42, 1293. doi: 10.1063/1.1696113
-
[36]
(36) Dunning, T. H. J. Chem. Phys. 1970, 53, 2823. doi: 10.1063/1.1674408
-
[37]
(37) Schneider, B.; Berman, H. M. Biophys. J. 1995, 69, 2661. doi: 10.1016/S0006-3495(95)80136-0
-
[38]
(38) Miertus, S.; Scrocco, E.; Tomasi, J. Chem. Phys. 1981, 55 (1),117. doi: 10.1016/0301-0104(81)85090-2
-
[39]
(39) Miertus, S.; Tomasi, J. Chem. Phys. 1982, 65 (2), 239. doi: 10.1016/0301-0104(82)85072-6
-
[40]
(40) Wang, H. Y.; Zhang, J. D.; Schaefer, H. F. Chem. Phys. Chem.2010, 11, 622. doi: 10.1002/cphc.200900687
-
[41]
(41) Noguera, M.; Sodupe, M.; Bertrán, J. Theor. Chem. Acc. 2007,118, 113. doi: 10.1007/s00214-007-0248-z
-
[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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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
-
[1]
Metrics
- PDF Downloads(442)
- Abstract views(750)
- HTML views(4)