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利用色散校正密度泛函理论精细调整水分子簇的分子间相互作用。

Fine Tuning the Intermolecular Interactions of Water Clusters Using the Dispersion-Corrected Density Functional Theory.

机构信息

Scuola Normale Superiore and CSGI, Classe di Scienze, Piazza dei Cavalieri 7, I-56126 Pisa, Italy.

Istituto Nazionale di Fisica Nucleare (INFN) Sezione di Pisa, Largo Bruno Pontecorvo 3, I-56127 Pisa, Italy.

出版信息

Molecules. 2023 Apr 30;28(9):3834. doi: 10.3390/molecules28093834.

DOI:10.3390/molecules28093834
PMID:37175249
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC10180381/
Abstract

Dispersion-inclusive density functional theory (DFT) methods have unequivocally demonstrated improved performances with respect to standard DFT approximations for modeling large and extended molecular systems at the quantum mechanical level. Yet, in some cases, disagreements with highly accurate reference calculations, such as CCSD(T) and quantum Monte Carlo (MC) calculations, still remain. Furthermore, the application of general-purpose corrections, such as the popular Grimme's semi-classical models (DFT-D), to different Kohn-Sham exchange-correlation functionals sometimes leads to variable and inconsistent results, which recommend a careful prior evaluation. In a recent study, we proposed a simple optimization protocol for enhancing the accuracy of these DFT-D methods by following an alternative and system-specific approach. Here, adopting the same computational strategy, we show how the accurate MC intermolecular interactions of a large set of water clusters of variable sizes (i.e., 300 (HO) structures, = 9, 15, 27) can be reproduced remarkably well by dispersion-corrected DFT models (i.e., B3LYP-D4, PBE-D4, revPBE(0)-D4) upon re-optimization, reaching a mean absolute error per monomer of ~0.1 kcal/mol. Hence, the obtained results support the use of this procedure for fine-tuning tailored DFT-D models for the accurate description of targeted molecular systems.

摘要

包含弥散修正的密度泛函理论(DFT)方法在对大尺寸、扩展分子体系进行量子力学水平建模方面,相较于标准 DFT 近似方法,表现出了明显的优越性。然而,在某些情况下,这些方法与高度精确的参考计算(如 CCSD(T)和量子蒙特卡罗(MC)计算)之间仍然存在分歧。此外,通常用途的校正(如 Grimme 的半经典模型(DFT-D))的应用,对于不同的 Kohn-Sham 交换相关泛函,有时会导致可变且不一致的结果,因此需要进行仔细的前期评估。在最近的一项研究中,我们提出了一种简单的优化方案,通过采用替代的、针对特定体系的方法,来提高这些 DFT-D 方法的准确性。在这里,我们采用相同的计算策略,展示了如何通过重新优化,使一系列具有可变尺寸(即 300 个(HO)结构, = 9、15、27)的大水簇的准确 MC 分子间相互作用,可以被修正后的弥散 DFT 模型(即 B3LYP-D4、PBE-D4、revPBE(0)-D4)很好地重现,达到每个单体的平均绝对误差约为 0.1 kcal/mol。因此,所得结果支持使用该程序对定制化的 DFT-D 模型进行微调,以准确描述目标分子体系。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b8e7/10180381/243b87bc79f8/molecules-28-03834-g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b8e7/10180381/f63f6d5ff8dd/molecules-28-03834-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b8e7/10180381/2ee63a8a640d/molecules-28-03834-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b8e7/10180381/372d67b2408d/molecules-28-03834-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b8e7/10180381/51268378735a/molecules-28-03834-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b8e7/10180381/243b87bc79f8/molecules-28-03834-g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b8e7/10180381/f63f6d5ff8dd/molecules-28-03834-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b8e7/10180381/2ee63a8a640d/molecules-28-03834-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b8e7/10180381/372d67b2408d/molecules-28-03834-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b8e7/10180381/51268378735a/molecules-28-03834-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b8e7/10180381/243b87bc79f8/molecules-28-03834-g005.jpg

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2
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Phys Chem Chem Phys. 2021 May 26;23(20):11635-11648. doi: 10.1039/d1cp01333e.
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A generally applicable atomic-charge dependent London dispersion correction.一种普遍适用的与原子电荷相关的伦敦色散校正。
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5
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6
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7
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8
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9
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10
Perspective: How good is DFT for water?观点:密度泛函理论对水的适用性如何?
J Chem Phys. 2016 Apr 7;144(13):130901. doi: 10.1063/1.4944633.