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Experimental log P values of SAMPL6 Part II log P challenge molecules

This directory contains the results of the log P measurements for 11 small molecules of SAMPL6 Part II log P challenge.

Experimental log P values were collected using potentiometric (pH-metric log P) measurements with a Sirius T3 instrument by Mehtap Isik from the Chodera Lab at MSKCC with the support of the Preformulation Group, Pharmaceutical Sciences, MRL, Merck & Co., Inc, especially Dorothy Levorse, Timothy Rhodes, and Brad Sherborne.

A minimum of 3 independent replicates of log P measurements were done for each molecule. Please see SAMPL6/logP Challenge Instructions/Experimental Details for more details about the experimental method.

The mean and standard error of the mean(SEM) of experimental octanol-water log P values were reported in logP_experimental_values.csv file, calculated as


The same batches of compounds as the pKa measurements for SAMPL6 pKa challenge were used for log P measurements. So, for purity information of analytes refer to SAMPL6/physical_properties/pKa/experimental_data/purity/ directory.

Aqueous pKa values of log P challenge compounds were previously determined using UV-metric measurements with the Sirius T3, as described in the SAMPL6 pKa challenge. These values were used as input for pH-metric log P measurements.


  • logP_experimental_values.csv - Mean and SEM of experimental log P values organized in a table for each molecule.
  • logP_results_of_replicate_experiments.csv - A table that contains experimental results of replicate log P measurements (N=3 or 4) and names of experimental reports (PDF files can be found in experiment_reports\ directory).
  • experiment_reports/ - This directory contains reports generated by Sirius T3 software for the results of log P measurements. Refer to logP_results_of_replicate_experiments.csv for matching SAMPL6 molecule IDs to names of the report files.
  • experimental_ID_and_SAMPL6_molecule_ID_table.csv - A table that matches experimental molecule IDs to SAMPL6 challenge molecule IDs.

Preprint on experimental log P measurements

Mehtap Işık, Dorothy Levorse, David L. Mobley, Timothy Rhodes, John D. Chodera. "Octanol-water partition coefficient measurements for the SAMPL6 Blind Prediction Challenge" bioRxiv 757393; doi:

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