Literature DB >> 27565796

Predicting cyclohexane/water distribution coefficients for the SAMPL5 challenge using MOSCED and the SMD solvation model.

Sebastian Diaz-Rodriguez1, Samantha M Bozada1, Jeremy R Phifer1, Andrew S Paluch2.   

Abstract

We present blind predictions using the solubility parameter based method MOSCED submitted for the SAMPL5 challenge on calculating cyclohexane/water distribution coefficients at 298 K. Reference data to parameterize MOSCED was generated with knowledge only of chemical structure by performing solvation free energy calculations using electronic structure calculations in the SMD continuum solvent. To maintain simplicity and use only a single method, we approximate the distribution coefficient with the partition coefficient of the neutral species. Over the final SAMPL5 set of 53 compounds, we achieved an average unsigned error of [Formula: see text] log units (ranking 15 out of 62 entries), the correlation coefficient (R) was [Formula: see text] (ranking 35), and [Formula: see text] of the predictions had the correct sign (ranking 30). While used here to predict cyclohexane/water distribution coefficients at 298 K, MOSCED is broadly applicable, allowing one to predict temperature dependent infinite dilution activity coefficients in any solvent for which parameters exist, and provides a means by which an excess Gibbs free energy model may be parameterized to predict composition dependent phase-equilibrium.

Entities:  

Keywords:  Distribution coefficient; Free energy of solvation; MOSCED; SAMPL5; SMD

Mesh:

Substances:

Year:  2016        PMID: 27565796     DOI: 10.1007/s10822-016-9945-9

Source DB:  PubMed          Journal:  J Comput Aided Mol Des        ISSN: 0920-654X            Impact factor:   3.686


  12 in total

1.  Prediction of SAMPL2 aqueous solvation free energies and tautomeric ratios using the SM8, SM8AD, and SMD solvation models.

Authors:  Raphael F Ribeiro; Aleksandr V Marenich; Christopher J Cramer; Donald G Truhlar
Journal:  J Comput Aided Mol Des       Date:  2010-04-01       Impact factor: 3.686

2.  Transferable potentials for phase equilibria. 9. Explicit hydrogen description of benzene and five-membered and six-membered heterocyclic aromatic compounds.

Authors:  Neeraj Rai; J Ilja Siepmann
Journal:  J Phys Chem B       Date:  2007-08-22       Impact factor: 2.991

3.  Performance of SM6, SM8, and SMD on the SAMPL1 test set for the prediction of small-molecule solvation free energies.

Authors:  Aleksandr V Marenich; Christopher J Cramer; Donald G Truhlar
Journal:  J Phys Chem B       Date:  2009-04-09       Impact factor: 2.991

4.  Universal solvation model based on solute electron density and on a continuum model of the solvent defined by the bulk dielectric constant and atomic surface tensions.

Authors:  Aleksandr V Marenich; Christopher J Cramer; Donald G Truhlar
Journal:  J Phys Chem B       Date:  2009-05-07       Impact factor: 2.991

5.  VMD: visual molecular dynamics.

Authors:  W Humphrey; A Dalke; K Schulten
Journal:  J Mol Graph       Date:  1996-02

6.  Predicting the excess solubility of acetanilide, acetaminophen, phenacetin, benzocaine, and caffeine in binary water/ethanol mixtures via molecular simulation.

Authors:  Andrew S Paluch; Sreeja Parameswaran; Shuai Liu; Anasuya Kolavennu; David L Mobley
Journal:  J Chem Phys       Date:  2015-01-28       Impact factor: 3.488

7.  Prediction of cyclohexane-water distribution coefficients with COSMO-RS on the SAMPL5 data set.

Authors:  Andreas Klamt; Frank Eckert; Jens Reinisch; Karin Wichmann
Journal:  J Comput Aided Mol Des       Date:  2016-07-26       Impact factor: 3.686

8.  Using MD Simulations To Calculate How Solvents Modulate Solubility.

Authors:  Shuai Liu; Shannon Cao; Kevin Hoang; Kayla L Young; Andrew S Paluch; David L Mobley
Journal:  J Chem Theory Comput       Date:  2016-03-02       Impact factor: 6.006

9.  Measuring experimental cyclohexane-water distribution coefficients for the SAMPL5 challenge.

Authors:  Ariën S Rustenburg; Justin Dancer; Baiwei Lin; Jianwen A Feng; Daniel F Ortwine; David L Mobley; John D Chodera
Journal:  J Comput Aided Mol Des       Date:  2016-10-07       Impact factor: 3.686

10.  Transferable potentials for phase equilibria. 10. Explicit-hydrogen description of substituted benzenes and polycyclic aromatic compounds.

Authors:  Neeraj Rai; J Ilja Siepmann
Journal:  J Phys Chem B       Date:  2012-12-21       Impact factor: 2.991

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  4 in total

1.  Combining MOSCED with molecular simulation free energy calculations or electronic structure calculations to develop an efficient tool for solvent formulation and selection.

Authors:  Courtney E Cox; Jeremy R Phifer; Larissa Ferreira da Silva; Gabriel Gonçalves Nogueira; Ryan T Ley; Elizabeth J O'Loughlin; Ana Karolyne Pereira Barbosa; Brett T Rygelski; Andrew S Paluch
Journal:  J Comput Aided Mol Des       Date:  2017-01-28       Impact factor: 3.686

2.  Blind prediction of cyclohexane-water distribution coefficients from the SAMPL5 challenge.

Authors:  Caitlin C Bannan; Kalistyn H Burley; Michael Chiu; Michael R Shirts; Michael K Gilson; David L Mobley
Journal:  J Comput Aided Mol Des       Date:  2016-09-27       Impact factor: 3.686

3.  A Comparison of QM/MM Simulations with and without the Drude Oscillator Model Based on Hydration Free Energies of Simple Solutes.

Authors:  Gerhard König; Frank C Pickard; Jing Huang; Walter Thiel; Alexander D MacKerell; Bernard R Brooks; Darrin M York
Journal:  Molecules       Date:  2018-10-19       Impact factor: 4.411

4.  Expanding the Solubility Parameter Method MOSCED to Pyridinium-, Quinolinium-, Pyrrolidinium-, Piperidinium-, Bicyclic-, Morpholinium-, Ammonium-, Phosphonium-, and Sulfonium-Based Ionic Liquids.

Authors:  Pratik Dhakal; Anthony R Weise; Martin C Fritsch; Cassandra M O'Dell; Andrew S Paluch
Journal:  ACS Omega       Date:  2020-02-19
  4 in total

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