Cargando…

A Promising Tool to Achieve Chemical Accuracy for Density Functional Theory Calculations on Y-NO Homolysis Bond Dissociation Energies

A DFT-SOFM-RBFNN method is proposed to improve the accuracy of DFT calculations on Y-NO (Y = C, N, O, S) homolysis bond dissociation energies (BDE) by combining density functional theory (DFT) and artificial intelligence/machine learning methods, which consist of self-organizing feature mapping neur...

Descripción completa

Detalles Bibliográficos
Autores principales: Li, Hong Zhi, Hu, Li Hong, Tao, Wei, Gao, Ting, Li, Hui, Lu, Ying Hua, Su, Zhong Min
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Molecular Diversity Preservation International (MDPI) 2012
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3430220/
https://www.ncbi.nlm.nih.gov/pubmed/22942689
http://dx.doi.org/10.3390/ijms13078051
_version_ 1782241914283622400
author Li, Hong Zhi
Hu, Li Hong
Tao, Wei
Gao, Ting
Li, Hui
Lu, Ying Hua
Su, Zhong Min
author_facet Li, Hong Zhi
Hu, Li Hong
Tao, Wei
Gao, Ting
Li, Hui
Lu, Ying Hua
Su, Zhong Min
author_sort Li, Hong Zhi
collection PubMed
description A DFT-SOFM-RBFNN method is proposed to improve the accuracy of DFT calculations on Y-NO (Y = C, N, O, S) homolysis bond dissociation energies (BDE) by combining density functional theory (DFT) and artificial intelligence/machine learning methods, which consist of self-organizing feature mapping neural networks (SOFMNN) and radial basis function neural networks (RBFNN). A descriptor refinement step including SOFMNN clustering analysis and correlation analysis is implemented. The SOFMNN clustering analysis is applied to classify descriptors, and the representative descriptors in the groups are selected as neural network inputs according to their closeness to the experimental values through correlation analysis. Redundant descriptors and intuitively biased choices of descriptors can be avoided by this newly introduced step. Using RBFNN calculation with the selected descriptors, chemical accuracy (≤1 kcal·mol(−1)) is achieved for all 92 calculated organic Y-NO homolysis BDE calculated by DFT-B3LYP, and the mean absolute deviations (MADs) of the B3LYP/6-31G(d) and B3LYP/STO-3G methods are reduced from 4.45 and 10.53 kcal·mol(−1) to 0.15 and 0.18 kcal·mol(−1), respectively. The improved results for the minimal basis set STO-3G reach the same accuracy as those of 6-31G(d), and thus B3LYP calculation with the minimal basis set is recommended to be used for minimizing the computational cost and to expand the applications to large molecular systems. Further extrapolation tests are performed with six molecules (two containing Si-NO bonds and two containing fluorine), and the accuracy of the tests was within 1 kcal·mol(−1). This study shows that DFT-SOFM-RBFNN is an efficient and highly accurate method for Y-NO homolysis BDE. The method may be used as a tool to design new NO carrier molecules.
format Online
Article
Text
id pubmed-3430220
institution National Center for Biotechnology Information
language English
publishDate 2012
publisher Molecular Diversity Preservation International (MDPI)
record_format MEDLINE/PubMed
spelling pubmed-34302202012-08-31 A Promising Tool to Achieve Chemical Accuracy for Density Functional Theory Calculations on Y-NO Homolysis Bond Dissociation Energies Li, Hong Zhi Hu, Li Hong Tao, Wei Gao, Ting Li, Hui Lu, Ying Hua Su, Zhong Min Int J Mol Sci Article A DFT-SOFM-RBFNN method is proposed to improve the accuracy of DFT calculations on Y-NO (Y = C, N, O, S) homolysis bond dissociation energies (BDE) by combining density functional theory (DFT) and artificial intelligence/machine learning methods, which consist of self-organizing feature mapping neural networks (SOFMNN) and radial basis function neural networks (RBFNN). A descriptor refinement step including SOFMNN clustering analysis and correlation analysis is implemented. The SOFMNN clustering analysis is applied to classify descriptors, and the representative descriptors in the groups are selected as neural network inputs according to their closeness to the experimental values through correlation analysis. Redundant descriptors and intuitively biased choices of descriptors can be avoided by this newly introduced step. Using RBFNN calculation with the selected descriptors, chemical accuracy (≤1 kcal·mol(−1)) is achieved for all 92 calculated organic Y-NO homolysis BDE calculated by DFT-B3LYP, and the mean absolute deviations (MADs) of the B3LYP/6-31G(d) and B3LYP/STO-3G methods are reduced from 4.45 and 10.53 kcal·mol(−1) to 0.15 and 0.18 kcal·mol(−1), respectively. The improved results for the minimal basis set STO-3G reach the same accuracy as those of 6-31G(d), and thus B3LYP calculation with the minimal basis set is recommended to be used for minimizing the computational cost and to expand the applications to large molecular systems. Further extrapolation tests are performed with six molecules (two containing Si-NO bonds and two containing fluorine), and the accuracy of the tests was within 1 kcal·mol(−1). This study shows that DFT-SOFM-RBFNN is an efficient and highly accurate method for Y-NO homolysis BDE. The method may be used as a tool to design new NO carrier molecules. Molecular Diversity Preservation International (MDPI) 2012-06-28 /pmc/articles/PMC3430220/ /pubmed/22942689 http://dx.doi.org/10.3390/ijms13078051 Text en © 2012 by the authors; licensee Molecular Diversity Preservation International, Basel, Switzerland. http://creativecommons.org/licenses/by/3.0 This article is an open-access article distributed under the terms and conditions of the Creative Commons Attribution license (http://creativecommons.org/licenses/by/3.0/).
spellingShingle Article
Li, Hong Zhi
Hu, Li Hong
Tao, Wei
Gao, Ting
Li, Hui
Lu, Ying Hua
Su, Zhong Min
A Promising Tool to Achieve Chemical Accuracy for Density Functional Theory Calculations on Y-NO Homolysis Bond Dissociation Energies
title A Promising Tool to Achieve Chemical Accuracy for Density Functional Theory Calculations on Y-NO Homolysis Bond Dissociation Energies
title_full A Promising Tool to Achieve Chemical Accuracy for Density Functional Theory Calculations on Y-NO Homolysis Bond Dissociation Energies
title_fullStr A Promising Tool to Achieve Chemical Accuracy for Density Functional Theory Calculations on Y-NO Homolysis Bond Dissociation Energies
title_full_unstemmed A Promising Tool to Achieve Chemical Accuracy for Density Functional Theory Calculations on Y-NO Homolysis Bond Dissociation Energies
title_short A Promising Tool to Achieve Chemical Accuracy for Density Functional Theory Calculations on Y-NO Homolysis Bond Dissociation Energies
title_sort promising tool to achieve chemical accuracy for density functional theory calculations on y-no homolysis bond dissociation energies
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3430220/
https://www.ncbi.nlm.nih.gov/pubmed/22942689
http://dx.doi.org/10.3390/ijms13078051
work_keys_str_mv AT lihongzhi apromisingtooltoachievechemicalaccuracyfordensityfunctionaltheorycalculationsonynohomolysisbonddissociationenergies
AT hulihong apromisingtooltoachievechemicalaccuracyfordensityfunctionaltheorycalculationsonynohomolysisbonddissociationenergies
AT taowei apromisingtooltoachievechemicalaccuracyfordensityfunctionaltheorycalculationsonynohomolysisbonddissociationenergies
AT gaoting apromisingtooltoachievechemicalaccuracyfordensityfunctionaltheorycalculationsonynohomolysisbonddissociationenergies
AT lihui apromisingtooltoachievechemicalaccuracyfordensityfunctionaltheorycalculationsonynohomolysisbonddissociationenergies
AT luyinghua apromisingtooltoachievechemicalaccuracyfordensityfunctionaltheorycalculationsonynohomolysisbonddissociationenergies
AT suzhongmin apromisingtooltoachievechemicalaccuracyfordensityfunctionaltheorycalculationsonynohomolysisbonddissociationenergies
AT lihongzhi promisingtooltoachievechemicalaccuracyfordensityfunctionaltheorycalculationsonynohomolysisbonddissociationenergies
AT hulihong promisingtooltoachievechemicalaccuracyfordensityfunctionaltheorycalculationsonynohomolysisbonddissociationenergies
AT taowei promisingtooltoachievechemicalaccuracyfordensityfunctionaltheorycalculationsonynohomolysisbonddissociationenergies
AT gaoting promisingtooltoachievechemicalaccuracyfordensityfunctionaltheorycalculationsonynohomolysisbonddissociationenergies
AT lihui promisingtooltoachievechemicalaccuracyfordensityfunctionaltheorycalculationsonynohomolysisbonddissociationenergies
AT luyinghua promisingtooltoachievechemicalaccuracyfordensityfunctionaltheorycalculationsonynohomolysisbonddissociationenergies
AT suzhongmin promisingtooltoachievechemicalaccuracyfordensityfunctionaltheorycalculationsonynohomolysisbonddissociationenergies