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首页> 外文期刊>Chemistry: A European journal >Nature of Base Stacking:Reference Quantum-Chemical Stacking Energies in Ten Unique B-DNA Base-Pair Steps
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Nature of Base Stacking:Reference Quantum-Chemical Stacking Energies in Ten Unique B-DNA Base-Pair Steps

机译：碱基堆积的性质：十个独特的B-DNA碱基配对步骤中的参考量子化学堆积能量

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摘要

Base-stacking energies in ten unique B-DNA base-pair steps and some other arrangements were evaluated by the second-order Moller-Plesset(MP2)method,complete basis set(CBS)extrapolation,and correction for triple(T)electron-correlation contributions.The CBS(T)calculations were compared with decade-old MP2/ 6-31G*(0.25)reference data and AMBER force field.The new calculations show modest increases in stacking stabilization compared to the MP2/6-31G*(0.25)data and surprisingly large sequence-dependent variation of stacking energies.The absolute force-field values are in better agreement with the new reference data,while relative discrepancies between quantum-chemical(QM)and force-field values increase modestly.Nevertheless,the force field provides good qualitative description of stacking,and there is no need to introduce additional pair-additive electrostatic terms,such as distributed mul-tipoles or out-of-plane charges.There is a rather surprising difference of about 0.1 A between the vertical separation of base pairs predicted by quantum chemistry and derived from crystal structures.Evaluations of different local arrangements of the 5'-CG-3' step indicate a sensitivity of the relative stacking energies to the level of calculation.Thus,describing quantitative relations between local DNA geometrical variations and stacking may be more complicated than usually assumed.The reference calculations are complemented by continuum-solvent assessment of solvent-screening effects.
机译：通过二阶Moller-Plesset（MP2）方法，完全基集（CBS）外推以及三重（T）电子校正，评估了十个独特的B-DNA碱基对步骤和一些其他排列中的碱基堆积能量。 CBS（T）计算与具有十年历史的MP2 / 6-31G *（0.25）参考数据和AMBER力场进行了比较。新计算显示出与MP2 / 6-31G *（ 0.25）数据以及令人惊讶的堆叠能量随序列的大变化。绝对力场值与新参考数据更好地吻合，而量子化学（QM）和力场值之间的相对差异适度增加。力场提供了良好的定性描述，无需引入额外的成对加性静电项，例如分布的多极子或平面外电荷。版本通过量子化学预测的且由晶体结构衍生的碱基对的理论分离。对5'-CG-3'步骤的不同局部排列的评估表明了相对堆积能对计算水平的敏感性。因此，描述了两者之间的定量关系。局部DNA的几何变化和堆积可能比通常假设的要复杂。参考计算得到溶剂筛选效果的连续溶剂评估的补充。

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