几何描述符作为非平面多环芳烃能量稳定性有效预测因子的大数据分析

IF 4.8 3区 化学 Q2 CHEMISTRY, MULTIDISCIPLINARY
Kasimir P. Gregory, Amir Karton
{"title":"几何描述符作为非平面多环芳烃能量稳定性有效预测因子的大数据分析","authors":"Kasimir P. Gregory,&nbsp;Amir Karton","doi":"10.1002/jcc.70198","DOIUrl":null,"url":null,"abstract":"<p>Accurate, efficient stability predictors are essential for understanding isomer formation in polycyclic aromatic hydrocarbons (PAHs), with implications for pollution toxicity and carbon-material design, holding broad environmental and technological significance. Recently, a benchmark study demonstrated that PBE0-D4 reproduces CCSD(T)-level isomerization energies for 335 PAHs with a mean absolute deviation (MAD) of 0.67 kcal mol<sup>−1</sup>. Here, we apply the PBE0-D4/6-31G(2df,p) level of theory to 38,264 PAH isomers from the COMPAS-3x database and identify fast, geometry-based parameters that predict isomer stability. The total dihedral deviation (Σ<sub>Dihedral</sub>) provides a cost-free nonplanarity metric yielding a mean absolute deviation (MAD) of 3.6 kcal mol<sup>−1</sup>, outperforming maximal <i>z</i>-displacement (MAD = 4.8 kcal mol<sup>−1</sup>) and the Harmonic Oscillator Model of Aromaticity (HOMA; MAD = 5.3 kcal mol<sup>−1</sup>). A combined Σ<sub>Dihedral</sub>–HOMA model reduces the MAD to 2.5 kcal mol<sup>−1</sup>, and adding a fitted semiempirical xTB correction further lowers the MAD to 0.8 kcal mol<sup>−1</sup>. We implement these descriptors in the PAH Automated Property Scanner (PAHAPS) web tool, enabling rapid estimation of PAH isomer energies from molecular coordinates without intensive quantum calculations. This integrated approach facilitates large-scale screening and efficient design of stable PAH isomers for environmental and materials applications.</p>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 21","pages":""},"PeriodicalIF":4.8000,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jcc.70198","citationCount":"0","resultStr":"{\"title\":\"Big-Data Analysis of Geometric Descriptors as Efficient Predictors of Energetic Stability in Nonplanar Polycyclic Aromatic Hydrocarbons\",\"authors\":\"Kasimir P. Gregory,&nbsp;Amir Karton\",\"doi\":\"10.1002/jcc.70198\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p>Accurate, efficient stability predictors are essential for understanding isomer formation in polycyclic aromatic hydrocarbons (PAHs), with implications for pollution toxicity and carbon-material design, holding broad environmental and technological significance. Recently, a benchmark study demonstrated that PBE0-D4 reproduces CCSD(T)-level isomerization energies for 335 PAHs with a mean absolute deviation (MAD) of 0.67 kcal mol<sup>−1</sup>. Here, we apply the PBE0-D4/6-31G(2df,p) level of theory to 38,264 PAH isomers from the COMPAS-3x database and identify fast, geometry-based parameters that predict isomer stability. The total dihedral deviation (Σ<sub>Dihedral</sub>) provides a cost-free nonplanarity metric yielding a mean absolute deviation (MAD) of 3.6 kcal mol<sup>−1</sup>, outperforming maximal <i>z</i>-displacement (MAD = 4.8 kcal mol<sup>−1</sup>) and the Harmonic Oscillator Model of Aromaticity (HOMA; MAD = 5.3 kcal mol<sup>−1</sup>). A combined Σ<sub>Dihedral</sub>–HOMA model reduces the MAD to 2.5 kcal mol<sup>−1</sup>, and adding a fitted semiempirical xTB correction further lowers the MAD to 0.8 kcal mol<sup>−1</sup>. We implement these descriptors in the PAH Automated Property Scanner (PAHAPS) web tool, enabling rapid estimation of PAH isomer energies from molecular coordinates without intensive quantum calculations. This integrated approach facilitates large-scale screening and efficient design of stable PAH isomers for environmental and materials applications.</p>\",\"PeriodicalId\":188,\"journal\":{\"name\":\"Journal of Computational Chemistry\",\"volume\":\"46 21\",\"pages\":\"\"},\"PeriodicalIF\":4.8000,\"publicationDate\":\"2025-08-01\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jcc.70198\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Journal of Computational Chemistry\",\"FirstCategoryId\":\"92\",\"ListUrlMain\":\"https://onlinelibrary.wiley.com/doi/10.1002/jcc.70198\",\"RegionNum\":3,\"RegionCategory\":\"化学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q2\",\"JCRName\":\"CHEMISTRY, MULTIDISCIPLINARY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Journal of Computational Chemistry","FirstCategoryId":"92","ListUrlMain":"https://onlinelibrary.wiley.com/doi/10.1002/jcc.70198","RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"CHEMISTRY, MULTIDISCIPLINARY","Score":null,"Total":0}
引用次数: 0

摘要

准确、高效的稳定性预测对于了解多环芳烃(PAHs)的异构体形成至关重要,对污染毒性和碳材料设计具有重要意义,具有广泛的环境和技术意义。最近,一项基准研究表明,PBE0-D4再现了335个多环芳烃的CCSD(T)级异构能,平均绝对偏差(MAD)为0.67 kcal mol−1。在这里,我们将PBE0-D4/6-31G(2df,p)水平的理论应用于compass -3x数据库中的38,264个多环芳烃异构体,并识别出快速的、基于几何的参数来预测异构体的稳定性。总二面体偏差(ΣDihedral)提供了一个无成本的非平面性度量,平均绝对偏差(MAD)为3.6 kcal mol - 1,优于最大z-位移(MAD = 4.8 kcal mol - 1)和芳香性谐振子模型(HOMA;MAD = 5.3 kcal mol−1)。结合ΣDihedral-HOMA模型将MAD降低到2.5 kcal mol - 1,并添加拟合的半经验xTB校正进一步将MAD降低到0.8 kcal mol - 1。我们在多环芳烃自动属性扫描器(PAHAPS)网络工具中实现了这些描述符,无需密集的量子计算就可以从分子坐标快速估计多环芳烃异构体的能量。这种综合方法有助于大规模筛选和有效设计稳定的多环芳烃异构体,用于环境和材料应用。
本文章由计算机程序翻译,如有差异,请以英文原文为准。

Big-Data Analysis of Geometric Descriptors as Efficient Predictors of Energetic Stability in Nonplanar Polycyclic Aromatic Hydrocarbons

Big-Data Analysis of Geometric Descriptors as Efficient Predictors of Energetic Stability in Nonplanar Polycyclic Aromatic Hydrocarbons

Accurate, efficient stability predictors are essential for understanding isomer formation in polycyclic aromatic hydrocarbons (PAHs), with implications for pollution toxicity and carbon-material design, holding broad environmental and technological significance. Recently, a benchmark study demonstrated that PBE0-D4 reproduces CCSD(T)-level isomerization energies for 335 PAHs with a mean absolute deviation (MAD) of 0.67 kcal mol−1. Here, we apply the PBE0-D4/6-31G(2df,p) level of theory to 38,264 PAH isomers from the COMPAS-3x database and identify fast, geometry-based parameters that predict isomer stability. The total dihedral deviation (ΣDihedral) provides a cost-free nonplanarity metric yielding a mean absolute deviation (MAD) of 3.6 kcal mol−1, outperforming maximal z-displacement (MAD = 4.8 kcal mol−1) and the Harmonic Oscillator Model of Aromaticity (HOMA; MAD = 5.3 kcal mol−1). A combined ΣDihedral–HOMA model reduces the MAD to 2.5 kcal mol−1, and adding a fitted semiempirical xTB correction further lowers the MAD to 0.8 kcal mol−1. We implement these descriptors in the PAH Automated Property Scanner (PAHAPS) web tool, enabling rapid estimation of PAH isomer energies from molecular coordinates without intensive quantum calculations. This integrated approach facilitates large-scale screening and efficient design of stable PAH isomers for environmental and materials applications.

求助全文
通过发布文献求助,成功后即可免费获取论文全文。 去求助
来源期刊
CiteScore
6.60
自引率
3.30%
发文量
247
审稿时长
1.7 months
期刊介绍: This distinguished journal publishes articles concerned with all aspects of computational chemistry: analytical, biological, inorganic, organic, physical, and materials. The Journal of Computational Chemistry presents original research, contemporary developments in theory and methodology, and state-of-the-art applications. Computational areas that are featured in the journal include ab initio and semiempirical quantum mechanics, density functional theory, molecular mechanics, molecular dynamics, statistical mechanics, cheminformatics, biomolecular structure prediction, molecular design, and bioinformatics.
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
确定
请完成安全验证×
copy
已复制链接
快去分享给好友吧!
我知道了
右上角分享
点击右上角分享
0
联系我们:info@booksci.cn Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。 Copyright © 2023 布克学术 All rights reserved.
京ICP备2023020795号-1
ghs 京公网安备 11010802042870号
Book学术文献互助
Book学术文献互助群
群 号:604180095
Book学术官方微信