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本文引用的文献

1
Comparison of some dispersion-corrected and traditional functionals with CCSD(T) and MP2 ab initio methods: dispersion, induction, and basis set superposition error.比较一些经分散修正和传统泛函与 CCSD(T)和 MP2 从头算方法：分散、诱导和基组超交误差。
J Chem Phys. 2012 Oct 7;137(13):134109. doi: 10.1063/1.4755990.
2
A reinvestigation of the dimer of para-benzoquinone and pyrimidine with MP2, CCSD(T), and DFT using functionals including those designed to describe dispersion.重新研究了对苯醌和嘧啶的二聚体，使用了包括旨在描述色散的函数在内的 MP2、CCSD(T) 和 DFT 方法。
J Phys Chem A. 2012 Aug 2;116(30):8100-5. doi: 10.1021/jp3050274. Epub 2012 Jul 19.
3
Aqueous solvation of polyalanine α-helices with specific water molecules and with the CPCM and SM5.2 aqueous continuum models using density functional theory.采用密度泛函理论，利用 CPCM 和 SM5.2 水连续体模型，研究了具有特定水分子的聚丙氨酸α-螺旋的水溶剂化。
J Phys Chem B. 2012 Feb 2;116(4):1437-45. doi: 10.1021/jp209177u. Epub 2012 Jan 23.
4
Cooperativity in long α- and 3(10)-helical polyalanines: both electrostatic and van der Waals interactions are essential.长 α-螺旋和 3(10)-螺旋聚丙氨酸中的协同性：静电相互作用和范德华相互作用都是必不可少的。
J Phys Chem B. 2011 Oct 6;115(39):11462-9. doi: 10.1021/jp203423w. Epub 2011 Sep 8.
5
Comparison of β-sheets of capped polyalanine with those of the tau-amyloid structures VQIVYK and VQIINK. A density functional theory study.用密度泛函理论研究封端聚丙氨酸β-折叠与 tau 淀粉样结构 VQIVYK 和 VQIINK 的比较。
J Phys Chem B. 2011 Sep 8;115(35):10560-6. doi: 10.1021/jp205388q. Epub 2011 Aug 11.
6
A comparison of the behavior of functional/basis set combinations for hydrogen-bonding in the water dimer with emphasis on basis set superposition error.氢键在水二聚体中功能/基组组合行为的比较，重点是基组叠加误差。
J Comput Chem. 2011 Jun;32(8):1519-27. doi: 10.1002/jcc.21729. Epub 2011 Feb 15.
7
Aggregation of capped hexaglycine strands into hydrogen-bonding motifs representative of pleated and rippled β-sheets, collagen, and polyglycine I and II crystal structures. A density functional theory study.六肽链帽状聚集形成氢键模体，代表折叠和波纹β-片层、胶原蛋白以及聚甘氨酸 I 和 II 晶体结构。密度泛函理论研究。
J Phys Chem B. 2011 Feb 17;115(6):1562-70. doi: 10.1021/jp111501d. Epub 2011 Jan 25.
8
Extended apolar beta-peptide foldamers: the role of axis chirality on beta-peptide sheet stability.伸展的非极性β-肽构象：轴手性对β-肽片层稳定性的作用。
J Phys Chem B. 2010 Jul 29;114(29):9338-48. doi: 10.1021/jp100955u.
9
Oscillations in meta-generalized-gradient approximation potential energy surfaces for dispersion-bound complexes.色散束缚复合物的元广义梯度近似势能面中的振荡。
J Chem Phys. 2009 Jul 21;131(3):034111. doi: 10.1063/1.3177061.
10
Long-range corrected hybrid density functionals with damped atom-atom dispersion corrections.具有阻尼原子-原子色散校正的长程校正杂化密度泛函
Phys Chem Chem Phys. 2008 Nov 28;10(44):6615-20. doi: 10.1039/b810189b. Epub 2008 Sep 29.

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.

DOI:10.1063/1.4737517
PMID:22852599
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC3416875/
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）。