Red-shifted hydrogen bonds and blue-shifted van der Waals contact in the standard Watson-Crick adenine-thymine base pair.
Red-shifted hydrogen bonds and blue-shifted van der Waals contact in the standard Watson-Crick adenine-thymine base pair.
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DOI：
10.1021/jp9035452
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发表时间：
2009-08
期刊：
影响因子：
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通讯作者：
P. Zhou;Wen-yuan Qiu
中科院分区：
文献类型：
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作者：
P. Zhou;Wen-yuan Qiu
用6-31G(d，p)基组的B3LYP泛函研究了Watson-Crick腺嘌呤-胸腺嘧啶(AT)标准碱基对，在该理论水平上AT碱基对的几何特征与实验最吻合。它同时表现出红移的N-H...O和N-H...N氢键以及蓝移的C-H...O接触。目的分析表明，蓝移的C-H…O接触以范德华相互作用的形式存在，并用反映键强度的电子密度Rho来解释红移和蓝移。通过NBO分析，我们提出了一种结合X-H(X=N，C)sigma键轨道的电子密度和sigma*反键轨道的电子密度来定量估计超共轭效应的方法。部分优化考虑了结构重组对红移和蓝移起源的影响，其在X-H(X=N，C)键上的行为是完全不同的。采用了复杂化和复极化模型，它们起到了缩短键的作用。静电吸引和Pauli/原子核斥力之间的竞争存在于两个典型的红移N-H…O和N-H…N氢键以及蓝移的C-H…O范德华接触中。H原子和Y原子(Y=O，N)之间的静电吸引是红移的重要原因，而H原子和O原子之间的核-核斥力可能是导致C-H键收缩和蓝移的一个因素。还讨论了受主O原子对C-H键的电场效应。
Standard Watson-Crick adenine-thymine (AT) base pair has been investigated by using the B3LYP functional with 6-31G(d, p) basis set, at which level of theory the geometrical characteristics of the AT base pair are the best in agreement with the experiment. It exhibits simultaneously red-shifted N-H...O and N-H...N hydrogen bonds as well as a blue-shifted C-H...O contact. AIM analysis suggests that the blue-shifted C-H...O contact exists as van der Waals interaction, and the electron density rho that reflects the strength of a bond has been used to explain the red- and blue-shifted. By means of NBO analysis, we report a method to estimate the effect of hyperconjugation quantitatively, which combines the electron density in the X-H (X = N, C) sigma bonding orbital with that in the sigma* antibonding orbital. The effect of structural reorganization on the origins of the red- and blue-shifted has been considered by the partial optimization, its behavior on the X-H (X = N, C) bond is quite different. Rehybridization and repolarization models are employed, and they act as bond-shortening effects. The competition between the electrostatic attractions and Pauli/nucleus repulsions is present in the two typical red-shifted N-H...O and N-H...N hydrogen bonds as well as in the blue-shifted C-H...O van der Waals contact. Electrostatic attraction between H and Y atoms (Y = O, N) is an important reason for the red shift, while the nucleus-nucleus repulsion between H and O atoms may be a factor leading to the C-H bond contraction and its blue shift. The electric field effect induced by the acceptor O atom on the C-H bond is also discussed.