BDE-db
A database of 290,664 bond dissociation energies for small molecules (10 or fewer heavy atoms) consisting of C, H, O, or N atoms. Enthalpy calculations were carried out using the M06-2X/def2-TZVP functional / basis set using Gaussian 16. Reported BDEs are in kcal/mol.
BDE-db
Publication:
Sowndarya S. V., S.; Kim, Y.; Kim, S.; St. John, P.; Paton, R. Expansion of Bond Dissociation Prediction with Machine Learning to Medicinally and Environmentally Relevant Chemical Space. Digit. Discovery, 2023, 2, 1900–1910. https://doi.org/10.1039/D3DD00169E
MARCEL
MARCEL is a PyTorch-based benchmark library that evaluates the potential of machine learning on conformer ensembles across a diverse set of molecules, datasets, and models.
Publication:
Zhu, Y.; Hwang, J.; Adams, K.; Liu, Z.; Nan, B.; Stenfors, B.; Du, Y.; Chauhan, J.; Wiest, O.; Isayev, O.; Coley, C. W.; Sun, Y.; Wang, W. Learning Over Molecular Conformer Ensembles: Datasets and Benchmarks. Int. Conf. Learn. Represent. (ICLR’24) 2024. https://sxkdz.github.io/files/publications/ICLR/MARCEL/MARCEL.pdf
MolPuzzle
MolPuzzle is a benchmark comprising 234 instances of structure elucidation, which feature over 18,000 QA samples presented in a sequential puzzle-solving process, involving three interlinked subtasks: molecule understanding, spectrum interpretation, and molecule construction.
MolPuzzle Github
Publication:
Guo, K.; Nan, B.; Zhou, Y.; Guo, T.; Guo, Z.; Surve, M.; Liang, Z.; Chawla, N. V.; Wiest, O.; Zhang, X. Can LLMs Solve Molecular Puzzles? A Multimodal Benchmark for Molecular Structure Elucidation. Adv. Neural Inf. Process. Syst. (NeurIPS24) 2024, 134721–134746. https://proceedings.neurips.cc/paper_files/paper/2024/file/f2b9e8e7a36d43ddfd3d55113d56b1e0-Paper-Datasets_and_Benchmarks_Track.pdf
Open Reaction Database
The Open Reaction Database (ORD) is an open-access schema and infrastructure for structuring and sharing organic reaction data, including a centralized data repository. The ORD schema supports conventional and emerging technologies, from benchtop reactions to automated high-throughput experiments and flow chemistry.
Open Reaction Database
Publications:
Kearnes SM, Maser MR, Wleklinski M, Kast A, Doyle AG, Dreher SD, Hawkins JM, Jensen KF, Coley CW. The Open Reaction Database. J. Am. Chem. Soc. 2021, 143, 18820-18826. doi.org/10.1021/jacs.1c09820
Mercado R, Kearnes SM, Coley C. Data Sharing in Chemistry: Lessons Learned and a Case for Mandating Structured Reaction Data. J. Chem. Inf. Model. 2023, 63, 4253-4265. doi.org/10.1021/acs.jcim.3c00607
Tutorial material:
ORD Tutorial