通过半实验和耦合簇模板片段,以 DFT 成本获得大分子的精确几何图形。

IF 5.7 1区 化学 Q2 CHEMISTRY, PHYSICAL
Journal of Chemical Theory and Computation Pub Date : 2024-10-22 Epub Date: 2024-10-07 DOI:10.1021/acs.jctc.4c00900
Silvia Di Grande, Federico Lazzari, Vincenzo Barone
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引用次数: 0

摘要

借助高分辨率光谱和精确的量子化学方法,我们可以获得气相中半刚性小分子的精确几何结构。这些结果可用于验证更便宜的低级量子化学模型或修正大分子的相应结构。有鉴于此,在这项工作中,我们利用文献中已有的大量半实验平衡结构来确认比萨复合方案(PCS2)版本的平均误差(键长为 1 mÅ,价角为 2 mrad),该方案适用于最多包含约 20 个原子的分子。然后,又在 PCS2 水平上优化了另外 30 个中型体系的几何结构,以涵盖一个更加均衡的化学空间,其中包含 SE 汇编中代表性较差的分子。最终的数据库可在公共域网站(https://www.skies-village.it/databases/)上查阅,并可用于校正在模板分子方法框架内通过混合或双杂交密度函数获得的较大分子的结构。多个实例表明,根据该数据库中的构筑模块结构进行修正,可将大分子的 B3LYP 几何参数误差减少近一个数量级,且不会增加计算成本。此外,不同密度泛函理论(DFT)或波函数(如 MP2)模型的结果也可以通过同样的方法得到改进,只需在所选水平上计算整个分子和合适的构筑模块即可。然后,当某些含有多达 20 个原子的构筑模块的参考结构不可用时,就可以利用合理的计算机资源,有目的地在 PCS2 水平上对其进行优化。因此,现在有了一种新的 DFT 成本工具,可供以实验为导向的科学家准确表征大分子。
本文章由计算机程序翻译,如有差异,请以英文原文为准。

Accurate Geometries of Large Molecules at DFT Cost by Semiexperimental and Coupled Cluster Templating Fragments.

Accurate Geometries of Large Molecules at DFT Cost by Semiexperimental and Coupled Cluster Templating Fragments.

Accurate geometries of small semirigid molecules in the gas phase are available thanks to high-resolution spectroscopy and accurate quantum chemical approaches. These results can be employed for validating cheaper low-level quantum chemical models or correcting the corresponding structures of large molecules. On these grounds, in this work, a large panel of semiexperimental equilibrium structures already available in the literature is used to confirm the average error (1 mÅ for bond lengths and 2 mrad for valence angles) of a version of the Pisa composite schemes (PCS2), which is applicable to molecules containing up to about 20 atoms. Then, the geometries of 30 additional medium-sized systems were optimized at the PCS2 level to cover a more balanced chemical space containing moieties poorly represented in SE compilations. The final database is available on a public domain Web site (https://www.skies-village.it/databases/) and can be employed for correcting structures of larger molecules obtained by hybrid or double-hybrid density functionals in the framework of the templating molecule approach. Several examples show that corrections based on the structures of building blocks taken from this database reduce the error of the B3LYP geometrical parameters of large molecules by nearly an order of magnitude without increasing the computational cost. Furthermore, the results of different density functional theory (DFT) or wave function (e.g., MP2) models can be improved in the same way by simply computing both the whole molecule and suitable building blocks at the chosen level. Then, whenever reference structures of some building blocks containing up to about 20 atoms are not available, they can be purposely optimized at the PCS2 level by employing reasonable computer resources. Therefore, a new DFT-cost tool is now available for the accurate characterization of large molecules by experiment-oriented scientists.

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来源期刊
Journal of Chemical Theory and Computation
Journal of Chemical Theory and Computation 化学-物理:原子、分子和化学物理
CiteScore
9.90
自引率
16.40%
发文量
568
审稿时长
1 months
期刊介绍: The Journal of Chemical Theory and Computation invites new and original contributions with the understanding that, if accepted, they will not be published elsewhere. Papers reporting new theories, methodology, and/or important applications in quantum electronic structure, molecular dynamics, and statistical mechanics are appropriate for submission to this Journal. Specific topics include advances in or applications of ab initio quantum mechanics, density functional theory, design and properties of new materials, surface science, Monte Carlo simulations, solvation models, QM/MM calculations, biomolecular structure prediction, and molecular dynamics in the broadest sense including gas-phase dynamics, ab initio dynamics, biomolecular dynamics, and protein folding. The Journal does not consider papers that are straightforward applications of known methods including DFT and molecular dynamics. The Journal favors submissions that include advances in theory or methodology with applications to compelling problems.
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