ArticleJournal of computer-aided molecular design2016
Calculating distribution coefficients based on multi-scale free energy simulations: an evaluation of MM and QM/MM explicit solvent simulations of water-cyclohexane transfer in the SAMPL5 challenge.
Article in Journal of computer-aided molecular design, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Advancing Rare-Earth Separation by Machine Learning.JACS Au · 2022Article
- Fragmentation Method for Computing Quantum Mechanics and Molecular Mechanics Gradients for Force Matching: Validation with Hydration Free Energy Predictions Using Adaptive Force Matching.The journal of physical chemistry. A · 2022Article
- Performing Molecular Dynamics Simulations and Computing Hydration Free Energies on the B3LYP-D3(BJ) Potential Energy Surface with Adaptive Force Matching: A Benchmark Study with Seven Alcohols and One Amine.ACS physical chemistry Au · 2021Article
- Rational prioritization strategy allows the design of macrolide derivatives that overcome antibiotic resistance.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- SAMPL7 blind challenge: quantum-mechanical prediction of partition coefficients and acid dissociation constants for small drug-like molecules.Journal of computer-aided molecular design · 2021Article
- On the faithfulness of molecular mechanics representations of proteins towards quantum-mechanical energy surfaces.Interface focus · 2020Article
- Quantum chemical predictions of water-octanol partition coefficients applied to the SAMPL6 logP blind challenge.Journal of computer-aided molecular design · 2020Article
- A deep learning approach for the blind logP prediction in SAMPL6 challenge.Journal of computer-aided molecular design · 2020Article
- Predicting partition coefficients of drug-like molecules in the SAMPL6 challenge with Drude polarizable force fields.Journal of computer-aided molecular design · 2020Article
- Use of Interaction Energies in QM/MM Free Energy Simulations.Journal of chemical theory and computation · 2019Article
- Molecular Dynamics Simulations of Membrane Permeability.Chemical reviews · 2019Review
- A Comparison of QM/MM Simulations with and without the Drude Oscillator Model Based on Hydration Free Energies of Simple Solutes.Molecules (Basel, Switzerland) · 2018Article
- On the convergence of multi-scale free energy simulations.Molecular simulation · 2018Article
- Quantum mechanical force fields for condensed phase molecular simulations.Journal of physics. Condensed matter : an Institute of Physics journal · 2017Article
- Blind prediction of cyclohexane-water distribution coefficients from the SAMPL5 challenge.Journal of computer-aided molecular design · 2016Article
- Blind prediction of distribution in the SAMPL5 challenge with QM based protomer and pKJournal of computer-aided molecular design · 2016Article
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12 authors.
Funding
Abstract
One of the central aspects of biomolecular recognition is the hydrophobic effect, which is experimentally evaluated by measuring the distribution coefficients of compounds between polar and apolar phases. We use our predictions of the distribution coefficients between water and cyclohexane from the SAMPL5 challenge to estimate the hydrophobicity of different explicit solvent simulation techniques. Based on molecular dynamics trajectories with the CHARMM General Force Field, we compare pure molecular mechanics (MM) with quantum-mechanical (QM) calculations based on QM/MM schemes that treat the solvent at the MM level. We perform QM/MM with both density functional theory (BLYP) and semi-empirical methods (OM1, OM2, OM3, PM3). The calculations also serve to test the sensitivity of partition coefficients to solute polarizability as well as the interplay of the quantum-mechanical region with the fixed-charge molecular mechanics environment. Our results indicate that QM/MM with both BLYP and OM2 outperforms pure MM. However, this observation is limited to a subset of cases where convergence of the free energy can be achieved.
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