文章基本信息

标题：A big data approach to the ultra-fast prediction of DFT-calculated bond energies
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作者：Xiaohui Qu ; Diogo ARS Latino ; Joao Aires-de-Sousa 等
期刊名称：Journal of Cheminformatics
印刷版ISSN：1758-2946
电子版ISSN：1758-2946
出版年度：2013
卷号：5
期号：1
页码：34
DOI：10.1186/1758-2946-5-34
语种：English
出版社：BioMed Central
摘要：The rapid access to intrinsic physicochemical properties of molecules is highly desired for large scale chemical data mining explorations such as mass spectrum prediction in metabolomics, toxicity risk assessment and drug discovery. Large volumes of data are being produced by quantum chemistry calculations, which provide increasing accurate estimations of several properties, e.g. by Density Functional Theory (DFT), but are still too computationally expensive for those large scale uses. This work explores the possibility of using large amounts of data generated by DFT methods for thousands of molecular structures, extracting relevant molecular properties and applying machine learning (ML) algorithms to learn from the data. Once trained, these ML models can be applied to new structures to produce ultra-fast predictions. An approach is presented for homolytic bond dissociation energy (BDE). Machine learning models were trained with a data set of >12,000 BDEs calculated by B3LYP/6-311++G(d,p)//DFTB. Descriptors were designed to encode atom types and connectivity in the 2D topological environment of the bonds. The best model, an Associative Neural Network (ASNN) based on 85 bond descriptors, was able to predict the BDE of 887 bonds in an independent test set (covering a range of 17.67–202.30 kcal/mol) with RMSD of 5.29 kcal/mol, mean absolute deviation of 3.35 kcal/mol, and R2 = 0.953. The predictions were compared with semi-empirical PM6 calculations, and were found to be superior for all types of bonds in the data set, except for O-H, N-H, and N-N bonds. The B3LYP/6-311++G(d,p)//DFTB calculations can approach the higher-level calculations B3LYP/6-311++G(3df,2p)//B3LYP/6-31G(d,p) with an RMSD of 3.04 kcal/mol, which is less than the RMSD of ASNN (against both DFT methods). An experimental web service for on-line prediction of BDEs is available at http://joao.airesdesousa.com/bde . Knowledge could be automatically extracted by machine learning techniques from a data set of calculated BDEs, providing ultra-fast access to accurate estimations of DFT-calculated BDEs. This demonstrates how to extract value from large volumes of data currently being produced by quantum chemistry calculations at an increasing speed mostly without human intervention. In this way, high-level theoretical quantum calculations can be used in large-scale applications that otherwise would not afford the intrinsic computational cost.
关键词：BDE ; Bond dissociation energy ; Neural network ; Random forest ; Machine learning ; Chemoinformatics ; DFT ; DFTB ; Big data