Acta Phys. -Chim. Sin. ›› 2014, Vol. 30 ›› Issue (2): 257-264.doi: 10.3866/PKU.WHXB201312031


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

WU Ying-Xi, WANG Hong-Yan, LIN Yue-Xia   

  1. School of Physical Science and Technology, Southwest Jiaotong University, Chengdu 610031, P. R. China
  • Received:2013-09-10 Revised:2013-12-03 Published:2014-01-23
  • Contact: WANG Hong-Yan
  • Supported by:

    The project was supported by the National Natural Science Foundation of China (10974161, 11174237), National Key Basic Research Program of China (973) (2013CB328904), and Application Basic Program of Sichuan Province, China (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.

Key words: Density functional theory, Base pair, Proton-transfer, First hydration shell, Bulk solvation effect


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