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Abstract Proton transfers are fundamental steps in polar reaction mechanisms. We generated a large dataset of over 51 million kinetically plausible proton transfer steps between heteroatoms from about 8,000 acids and conjugate bases with experimental aqueous pKas, spanning pKavalues from −15 to +37. Rate factors were estimated at 25 °C using a simplified Eigen equation with pKas but without statistical factors. Steps with estimated rate constants ≥ 103M−1s−1were included in the final dataset. Additionally, 5,043 proton transfer steps from carbon acids to heteroatom bases were estimated using the Eigen-Bernasconi equation based on reported intrinsic rate constants and Brønsted β values. Carbon proton transfers with rate constants ≥ 103 M−1s−1were added to the final dataset. Each entry was encoded in SMIRKS format with electron-flow specification for machine learning compatibility. Diversity of structure was prioritized over diversity of conditions; calculated rate constants are expected to be accurate in aqueous environments. This approach and dataset should prove valuable for training models to predict stepwise mechanistic pathways.
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Plausible Proton Transfer Data Files
A zipped file containing:51M_Heteroatom.csv - 51M proton transfer steps from heteroatom acids to heteroatom bases, with SMIRKS, calculated log k1, and pKas,5KCarbonPT.csv - 5K proton transfer steps from carbon acids to heteroatom bases, with SMIRKS, calculated log k1, and pKas, Brønsted β values, statistical factors (qB, pB, qC, pC) intrinsic rate constants (ko),49ExperimentalCarbonPT.csv - 49 proton transfers from heteroatom acids to carbon bases in SMIRKS format, with experimentally measured log k1, and literature references.51M_heteroatom_raw – a subfolder with two files containing lists of 7.6K heteroatomic acids and bases in SMILES format with the acidic and basic atoms labeled, with pKas, literature references: Acid.csv, ConBase.csv100_Heteroatom.csv - A representative sample set of 100 out of the 51M proton transfer steps100K_Heteroatom.csv - A representative sample set of 100,000 out of the 51M proton transfer stepscarbon_acid_raw – a subfolder containing a list of intrinsic rate constants for carbon acids in SMILES format, with statistical factors (Carbon_Acids.csv) and a subfolder named Bases containing seven lists of heteroatom base classes (ArO-.csv, R2NH.csv, R3N.csv, “RCO2- and ArCO2-.csv”, RNH2.csv, RO-.csv and RS-.csv). Lists of heteroatom bases are in SMILES format, sectioned by class and with statistical factors, selected from the Heteroatom set
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- Award ID(s):
- 1955811
- PAR ID:
- 10670686
- Publisher / Repository:
- figshare
- Date Published:
- Subject(s) / Keyword(s):
- Organic chemistry not elsewhere classified Physical organic chemistry
- Format(s):
- Medium: X Size: 943147581 Bytes
- Size(s):
- 943147581 Bytes
- Sponsoring Org:
- National Science Foundation
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