Table 5. Predicted log P values of free energy calculations of methods using GAFF, TIP3P water, and dry octanol.
The methods listed are the reference direct transfer free energy (DFE) protocol, reference indirect solvation-based transfer free energy (IFE) protocol and submission sqosi (MD-AMBER-dryoct). Details of the two reference protocols can be found in Section 12.1. log P predictions for multiple tautomers (SM08) and resonance structures (SM11 and SM14) are listed, when available. The experimental values are provided for comparison. The same experimental P log values are stated for multiple tautomers or resonance structures. Potentiometric log P measurements do not provide information about the identity or populations of tautomers.
| Molecule | Indirect Solvation-Based Transfer Free Energy (IFE) Protocol | REF07 Direct Transfer Free Energy (DFE) Protocol | sqosi (MD-AMBER-dryoct) | Experimental |
|---|---|---|---|---|
| SM02 | 7.6±0.3 | 5.5±0.1 | 5.3±0.3 | 4.09±0.03 |
| SM04 | 6.2±0.4 | 5.2±0.1 | 5.9±0.3 | 3.98±0.03 |
| SM07 | 4.3±0.2 | 4.2±0.3 | 4.8±0.4 | 3.21±0.04 |
| SM081,2 | 2.8±0.2 | 9.8±0.1 | 3.10±0.03 | |
| SM08_micro008 | 5.5±0.6 | 3.8±0.1 | 3.10±0.03 | |
| SM08_micro010 | 3.9±0.3 | 3.7±0.2 | 5.9±0.4 | 3.10±0.03 |
| SM09 | 3.1 ±0.4 | 4.51 ±0.03 | 4.0±0.3 | 3.0±0.1 |
| SM111 | 1.6±0.4 | 2.5±0.1 | 2.10±0.04 | |
| SM11_micro005 | 2.9±0.3 | 2.36±0.01 | 2.3±0.3 | 2.10±0.04 |
| SM12 | 4.9±0.3 | 5.6±0.1 | 5.2±0.3 | 3.83±0.03 |
| SM13 | 5.1 ±0.3 | 5.3±0.1 | 6.0±0.5 | 2.92±0.04 |
| SM141 | 2.2±0.2 | 2.4±0.1 | 1.95±0.03 | |
| SM14_micro001 | 2.8±0.2 | 3.1 ±0.1 | 2.5±0.3 | 1.95±0.03 |
| SM15 | 2.7±0.2 | 3.1 ±0.1 | 3.0±0.2 | 3.07±0.03 |
| SM16 | 4.3±0.3 | 3.9±0.1 | 4.6±0.4 | 2.62±0.01 |
The tautomer or resonance structure presented as the input SMILES for the SAMPL6 log P Challenge.
It corresponds to the microstate SM08_micro011 of the SAMPL6 pKa Challenge.