ArticleJournal of chemical theory and computation2016
Calculating Partition Coefficients of Small Molecules in Octanol/Water and Cyclohexane/Water.
Article in Journal of chemical theory and computation, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 69 papers.
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Who cites it
69 citing papers in PubMed.
- A Box-Behnken-Optimized Phytosomal Strategy for Diosgenin: Enhancing Oral Delivery and Antipsoriatic Efficacy in a Preclinical Model.ACS omega · 2026Article
- Dual-Coordinate Relative Free Energy Simulations Using Machine-Learned Interatomic Potentials.Journal of chemical theory and computation · 2026Article
- Toward the Engineering of Chameleonicity: Quantum Mechanical Prediction for the Octanol/Water Distributions of Large Flexible Triazine Macrocycles.Journal of chemical information and modeling · 2026Article
- Molecular determinants of arginine versus lysine cation-π interactions in biomolecular condensates.Communications chemistry · 2026Article
- Graph-based transformer to predict the octanol-water partition coefficient.Journal of cheminformatics · 2026Article
- Article
- Architecture-Independent Absolute Solvation Free Energy Calculations with Neural Network Potentials.The journal of physical chemistry letters · 2025Article
- Automated parametrization of small molecules within the Martini 3 coarse-grained model guided by experimental log P values.Scientific reports · 2025Article
- Quantification of Small Molecule Partitioning in a Biomolecular Condensate with 2D Nuclear Magnetic Resonance Spectroscopy.Chembiochem : a European journal of chemical biology · 2025Article
- Multi-fidelity graph neural networks for predicting toluene/water partition coefficients.Journal of cheminformatics · 2025Article
- Predicting Distribution Coefficients (LogD) of Cyclic Peptides Using Molecular Dynamics Simulations.Pharmaceutical research · 2025Article
- Validation of a Coarse-Grained Martini 3 Model for Molecular Oxygen.Journal of chemical theory and computation · 2025Article
- Predicting absolute aqueous solubility by applying a machine learning model for an artificially liquid-state as proxy for the solid-state.Journal of computer-aided molecular design · 2023Article
- Integrated Molecular Modeling and Machine Learning for Drug Design.Journal of chemical theory and computation · 2023Review
- Energy-entropy multiscale cell correlation method to predict toluene-water logPhysical chemistry chemical physics : PCCP · 2023Article
- Repurposing miconazole and tamoxifen for the treatment of Mycobacterium abscessus complex infections through in silico chemogenomics approach.World journal of microbiology & biotechnology · 2023Article
- Coarse-grained modeling of polystyrene-modified CNTs and their interactions with lipid bilayers.Biophysical journal · 2023Article
- Development and test of highly accurate endpoint free energy methods. 2: Prediction of logarithm of n-octanol-water partition coefficient (logP) for druglike molecules using MM-PBSA method.Journal of computational chemistry · 2023Article
- Efficient screening of protein-ligand complexes in lipid bilayers using LoCoMock score.Journal of computer-aided molecular design · 2023Article
- Partitioning of Antioxidants in Edible Oil-Water Binary Systems and in Oil-in-Water Emulsions.Antioxidants (Basel, Switzerland) · 2023Review
9 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
Partition coefficients describe how a solute is distributed between two immiscible solvents. They are used in drug design as a measure of a solute's hydrophobicity and a proxy for its membrane permeability. We calculate partition coefficients from transfer free energies using molecular dynamics simulations in explicit solvent. Setup is done by our new Solvation Toolkit which automates the process of creating input files for any combination of solutes and solvents for many popular molecular dynamics software packages. We calculate partition coefficients between octanol/water and cyclohexane/water with the Generalized AMBER Force Field (GAFF) and the Dielectric Corrected GAFF (GAFF-DC). With similar methods in the past we found a root-mean-squared error (RMSE) of 6.3 kJ/mol in hydration free energies which would correspond to an error of around 1.6 log units in partition coefficients if solvation free energies in both solvents were estimated with comparable accuracy. Here we find an overall RMSE of about 1.2 log units with both force fields. Results from GAFF and GAFF-DC seem to exhibit systematic biases in opposite directions for calculated cyclohexane/water partition coefficients.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.