比较一些用于肽和环己烷衍生物构象的分散校正和传统函数。
Comparison of some dispersion-corrected and traditional functionals as applied to peptides and conformations of cyclohexane derivatives.
机构信息
Department of Chemistry, City University of New York - Hunter College and the Graduate School, 695 Park Avenue, New York, New York 10065, USA.
出版信息
J Chem Phys. 2012 Jul 28;137(4):044109. doi: 10.1063/1.4737517.
Abstract
We compare the energetic and structural properties of fully optimized α-helical and antiparallel β-sheet polyalanines and the energetic differences between axial and equatorial conformations of three cyclohexane derivatives (methyl, fluoro, and chloro) as calculated using several functionals designed to treat dispersion (B97-D, ωB97x-D, M06, M06L, and M06-2X) with other traditional functionals not specifically parametrized to treat dispersion (B3LYP, X3LYP, and PBE1PBE) and with experimental results. Those functionals developed to treat dispersion significantly overestimate interaction enthalpies of folding for the α-helix and predict unreasonable structures that contain Ramachandran φ and ψ and C = O...N H-bonding angles that are out of the bounds of databases compiled the β-sheets. These structures are consistent with overestimation of the interaction energies. For the cyclohexanes, these functionals overestimate the stabilities of the axial conformation, especially when used with smaller basis sets. Their performance improves when the basis set is improved from D95∗∗ to aug-cc-pVTZ (which would not be possible with systems as large as the peptides).
摘要
我们比较了全优化的α-螺旋和反平行β-折叠聚丙氨酸的能量和结构性质，以及三种环己烷衍生物（甲基、氟和氯）轴向和赤道构象之间的能量差异，这些计算使用了几种旨在处理色散的函数（B97-D、ωB97x-D、M06、M06L 和 M06-2X）以及其他未专门针对色散进行参数化的传统函数（B3LYP、X3LYP 和 PBE1PBE）与实验结果进行比较。那些旨在处理色散的功能明显高估了折叠的α-螺旋的相互作用焓，并预测了不合理的结构，其中包含超出β-折叠数据库中编译的 Ramachandran φ 和 ψ 以及 C = O...N H 键角度的范围。这些结构与相互作用能的高估一致。对于环己烷，这些功能高估了轴向构象的稳定性，尤其是在使用较小的基组时。当从 D95∗∗基组改进到 aug-cc-pVTZ 基组时，它们的性能会提高（对于像肽这样大的系统，这是不可能的）。
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