Partitioning of Alkane and Alcohol Solutes between Water and (Dry or Wet) 1-Octanol

Chen, Bin; Siepmann, J. Ilja

doi:10.1021/ja001120+

Cited by 64 publications

(68 citation statements)

References 30 publications

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“…These methods include quantitative structure-property relationships (QSPR) [6,7]; and atom-based [8], and quantum chemistry motivated methods such as COSMOtherm/COSMO-RS [9][10][11]. Computer simulations, e. g. molecular dynamics (MD) or Monte Carlo (MC) methods using atom-based potential functions or coarse-grained force-fields such as the MARTINI force field [12], provide an additional route to the prediction of log P for small or medium size solute molecules [13][14][15][16][17][18][19][20][21][22][23][24][25][26][27][28][29]. There have also been attempts to use multiscale simulation methods mixing atomistic and coarse-grained potentials [13,30].…”

Section: Partition Coefficientsmentioning

confidence: 99%

Dissipative particle dynamics: Systematic parametrization using water-octanol partition coefficients

Anderson

Bray

Ferrante³

et al. 2017

The Journal of Chemical Physics

215

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We present a systematic, top-down, thermodynamic parametrization scheme for dissipative particle dynamics (DPD) using water-octanol partition coefficients, supplemented by water-octanol phase equilibria and pure liquid phase density data. We demonstrate the feasibility of computing the required partition coefficients in DPD using brute-force simulation, within an adaptive semi-automatic staged optimization scheme. We test the methodology by fitting to experimental partition coefficient data for twenty one small molecules in five classes comprising alcohols and poly-alcohols, amines, ethers and simple aromatics, and alkanes (i.e., hexane). Finally, we illustrate the transferability of a subset of the determined parameters by calculating the critical micelle concentrations and mean aggregation numbers of selected alkyl ethoxylate surfactants, in good agreement with reported experimental values.

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Section: Partition Coefficientsmentioning

confidence: 99%

Dissipative particle dynamics: Systematic parametrization using water-octanol partition coefficients

Anderson

Bray

Ferrante³

et al. 2017

The Journal of Chemical Physics

215

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“…Another method for the calculation of absolute free energies of transfer and partition coefficients is Gibbs ensemble Monte Carlo (GEMC). 43,44 In GEMC, two condensed phases are simulated concurrently and attempts are made periodically to "swap" the solute of interest between phases. The free energy of transfer is determined simply as the ratio of the number density of the solute in each phase 45…”

Section: Introductionmentioning

confidence: 99%

Direct calculation of 1-octanol–water partition coefficients from adaptive biasing force molecular dynamics simulations

Bhatnagar

Kamath

Chelst

et al. 2012

The Journal of Chemical Physics

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The 1-octanol-water partition coefficient log K(ow) of a solute is a key parameter used in the prediction of a wide variety of complex phenomena such as drug availability and bioaccumulation potential of trace contaminants. In this work, adaptive biasing force molecular dynamics simulations are used to determine absolute free energies of hydration, solvation, and 1-octanol-water partition coefficients for n-alkanes from methane to octane. Two approaches are evaluated; the direct transfer of the solute from 1-octanol to water phase, and separate transfers of the solute from the water or 1-octanol phase to vacuum, with both methods yielding statistically indistinguishable results. Calculations performed with the TIP4P and SPC∕E water models and the TraPPE united-atom force field for n-alkanes show that the choice of water model has a negligible effect on predicted free energies of transfer and partition coefficients for n-alkanes. A comparison of calculations using wet and dry octanol phases shows that the predictions for log K(ow) using wet octanol are 0.2-0.4 log units lower than for dry octanol, although this is within the statistical uncertainty of the calculation.

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“…While other approaches have been used to calculate solvation free energies, 40 alchemical free energy calculations using explicit solvent have become a mainstream approach, 41,42 in part because of their formal rigor. Alternative approaches include implicit solvent models, [34][35][36][37]43 which yield ∆G hyd but do not take into consideration solvent configuration around the solute, and Monte Carlo based approaches using the Gibbs ensemble [44][45][46][47][48][49][50] and expanded ensemble, 51 though these are most commonly used for molecules that are particularly small and/or rigid.…”

Section: Introductionmentioning

confidence: 99%

Approaches for calculating solvation free energies and enthalpies demonstrated with an update of the FreeSolv database

Matos

Kyu

Loeffler³

et al. 2017

Preprint

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Solvation free energies can now be calculated precisely from molecular simulations, providing a valuable test of the energy functions underlying these simulations. Here, we briefly review "alchemical" approaches for calculating the solvation free energies of small, neutral organic molecules from molecular simulations, and illustrate by applying them to calculate aqueous solvation free energies (hydration free energies). These * To whom correspondence should be addressed † University of California, Irvine ‡ University of California, Irvine ¶ STFC Daresbury, Warrington, WA4 4AD, United Kingdom § Memorial Sloan Kettering Cancer Center, New York University of Colorado, Boulder ⊥ University of California, Irvine 30, 2017; approaches use a non-physical pathway to compute free energy differences from a simulation or set of simulations and appear to be a particularly robust and general-purpose approach for this task. We also present an update (version 0.5) to our FreeSolv database of experimental and calculated hydration free energies of neutral compounds and provide input files in formats for several simulation packages. This revision to FreeSolv provides calculated values generated with a single protocol and software version, rather than the heterogeneous protocols used in the prior version of the database. We also further update the database to provide calculated enthalpies and entropies of hydration and some experimental enthalpies and entropies, as well as electrostatic and nonpolar components of solvation free energies.International license peer-reviewed) is the author/funder. It is made available under a The copyright holder for this preprint (which was not . http://dx.doi.org/10.1101/104281 doi: bioRxiv preprint first posted online Jan.

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Partitioning of Alkane and Alcohol Solutes between Water and (Dry or Wet) 1-Octanol

Cited by 64 publications

References 30 publications

Dissipative particle dynamics: Systematic parametrization using water-octanol partition coefficients

Dissipative particle dynamics: Systematic parametrization using water-octanol partition coefficients

Direct calculation of 1-octanol–water partition coefficients from adaptive biasing force molecular dynamics simulations

Approaches for calculating solvation free energies and enthalpies demonstrated with an update of the FreeSolv database

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