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Quantum Chemical Calculations for over 200,000 Organic Radical Species and 40,000 Associated Closed-shell Molecules

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Journal Sci Data
Specialty Science
Date 2020 Jul 23
PMID 32694541
Citations 24
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Abstract

The stabilities of radicals play a central role in determining the thermodynamics and kinetics of many reactions in organic chemistry. In this data descriptor, we provide consistent and validated quantum chemical calculations for over 200,000 organic radical species and 40,000 associated closed-shell molecules containing C, H, N and O atoms. These data consist of optimized 3D geometries, enthalpies, Gibbs free energy, vibrational frequencies, Mulliken charges and spin densities calculated at the M06-2X/def2-TZVP level of theory, which was previously found to have a favorable trade-off between experimental accuracy and computational efficiency. We expect this data to be useful in the further development of machine learning techniques to predict reaction pathways, bond strengths, and other phenomena closely related to organic radical chemistry.

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References
1.
Kim S, Chen J, Cheng T, Gindulyte A, He J, He S . PubChem 2019 update: improved access to chemical data. Nucleic Acids Res. 2018; 47(D1):D1102-D1109. PMC: 6324075. DOI: 10.1093/nar/gky1033. View

2.
Riniker S, Landrum G . Better Informed Distance Geometry: Using What We Know To Improve Conformation Generation. J Chem Inf Model. 2015; 55(12):2562-74. DOI: 10.1021/acs.jcim.5b00654. View

3.
Faber F, Hutchison L, Huang B, Gilmer J, Schoenholz S, Dahl G . Prediction Errors of Molecular Machine Learning Models Lower than Hybrid DFT Error. J Chem Theory Comput. 2017; 13(11):5255-5264. DOI: 10.1021/acs.jctc.7b00577. View

4.
Schutt K, Arbabzadah F, Chmiela S, Muller K, Tkatchenko A . Quantum-chemical insights from deep tensor neural networks. Nat Commun. 2017; 8:13890. PMC: 5228054. DOI: 10.1038/ncomms13890. View

5.
OBoyle N, Banck M, James C, Morley C, Vandermeersch T, Hutchison G . Open Babel: An open chemical toolbox. J Cheminform. 2011; 3:33. PMC: 3198950. DOI: 10.1186/1758-2946-3-33. View