Base stacking in cytosine dimer. A comparison of correlated ab initio calculations with three empirical potential models and density functional theory calculations
Base stacking in cytosine dimer. A comparison of correlated ab initio calculations with three empirical potential models and density functional theory calculations
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胞嘧啶二聚体中的碱基堆积。
DOI：
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发表时间：
1996
影响因子：
3
通讯作者：
P. Hobza
中科院分区：
文献类型：
--
作者：
J. Šponer;J. Leszczynski;P. Hobza
从头算计算了80多种构型的胞嘧啶二聚体的MP2/6-31G*相互作用能。利用扩散偏振函数适当地覆盖了色散能量。将从头计算的结果与由Lennard-Jones势(包括色散和排斥贡献)和静电项构成的三个静电经验势模型的计算结果进行了比较。在MP2/6-31G*理论水平上，还得到了静电项的点电荷和点多极。点电荷MEP模型(由分子静电势得到的原子电荷)令人满意地再现了从头计算数据。在胞嘧啶平面以下和上方添加π电荷并不影响计算的能量。与MEP方法相比，采用分布式多极分析的模型与从头计算数据的一致性较差。MP2MEP电荷也是使用更大的原子轨道：cc-pVDZ，6-311+G(2d，p)和aug-cc-pVDZ得到的。用这三组点电荷计算的相互作用能与MP2/6-31G*电荷的相互作用能之差小于0.8千卡/摩尔。并与密度泛函理论(DFT)方法进行了比较。密度泛函理论计算很好地再现了相互作用能的静电部分。它们还涵盖了一些经验电势不能再现的非静电短程效应。DFT方法不包括色散能。因此，这一由经验项近似的能量被添加到DFT相互作用能中。对于3.9-4.0的碱基垂直间隔，所产生的相互作用能量表现出次要的伪影最小值。这一缺陷是DFT泛函固有的，因为在Hartree-Fock+色散相互作用能量中没有观察到它。
Ab initio MP2/6‐31G* interaction energies were calculated for more than 80 geometries of stacked cytosine dimer. Diffuse polarization functions were used to properly cover the dispersion energy. The results of ab initio calculations were compared with those obtained from three electrostatic empirical potential models, constructed as the sum of a Lennard‐Jones potential (covering dispersion and repulsion contributions) and the electrostatic term. Point charges and point multipoles of the electrostatic term were also obtained at the MP2/6‐31G* level of theory. The point charge MEP model (atomic charges derived from molecular electrostatic potential) satisfactorily reproduced the ab initio data. Addition of π‐charges localized below and above the cytosine plane did not affect the calculated energies. The model employing the distributed multipole analysis gave worse agreement with the ab initio data than the MEP approach. The MP2 MEP charges were also derived using larger sets of atomic orbitals: cc‐pVDZ, 6‐311 + G(2d, p), and aug‐cc‐pVDZ. Differences between interaction energies calculated using these three sets of point charges and the MP2/6‐31G* charges were smaller than 0.8 kcal/mol. The correlated ab initio calculations were also compared with the density functional theory (DFT) method. DFT calculations well reproduced the electrostatic part of interaction energy. They also covered some nonelectrostatic short‐range effects which were not reproduced by the empirical potentials. The DFT method does not include the dispersion energy. This energy, approximated by an empirical term, was therefore added to the DFT interaction energy. The resulting interaction energy exhibited an artifact secondary minimum for a 3.9‐4.0 vertical separation of bases. This defect is inherent in the DFT functionals, because it is not observed for the Hartree‐Fock + dispersion interaction energy.© 1996 John Wiley & Sons, Inc.
DNA螺旋结构的起源及其序列依赖性。
影响因子：
2.9
作者：
Sarai,A;Mazur,J;Nussinov,R;Jernigan,RL
通讯作者：
Jernigan,RL