Literature DB >> 26010106

Force Field Benchmark of Organic Liquids. 2. Gibbs Energy of Solvation.

Jin Zhang1,2, Badamkhatan Tuguldur2,3, David van der Spoel2.   

Abstract

Quantitative prediction of physical properties of liquids is a longstanding goal of molecular simulation. Here, we evaluate the predictive power of the Generalized Amber Force Field (Wang et al. J. Comput. Chem. 2004, 25, 1157-1174) for the Gibbs energy of solvation of organic molecules in organic solvents using the thermodynamics integration (TI) method. The results are compared to experimental data, to a model based on quantitative structure property relations (QSPR), and to the conductor-like screening models for realistic solvation (COSMO-RS) model. Although the TI calculations yield slightly better correlation to experimental results than the other models, in all fairness we should conclude that the difference between the models is minor since both QSPR and COSMO-RS yield a slightly lower RMSD from that of the experiment (<3.5 kJ/mol). By analyzing which molecules (either as solvents or solutes) are outliers in the TI calculations, we can pinpoint where additional parametrization efforts are needed. For the force field based TI calculations, deviations from the experiment occur in particular when compounds containing nitro or ester groups are solvated into other liquids, suggesting that the interaction between these groups and solvents may be too strong. In the COSMO-RS calculations, outliers mainly occur when compounds containing (in particular aromatic) rings are solvated despite using a ring correction term in the calculations.

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Year:  2015        PMID: 26010106     DOI: 10.1021/acs.jcim.5b00106

Source DB:  PubMed          Journal:  J Chem Inf Model        ISSN: 1549-9596            Impact factor:   4.956


  16 in total

1.  Calculating Partition Coefficients of Small Molecules in Octanol/Water and Cyclohexane/Water.

Authors:  Caitlin C Bannan; Gaetano Calabró; Daisy Y Kyu; David L Mobley
Journal:  J Chem Theory Comput       Date:  2016-08-01       Impact factor: 6.006

Review 2.  Microscopic Characterization of Membrane Transporter Function by In Silico Modeling and Simulation.

Authors:  J V Vermaas; N Trebesch; C G Mayne; S Thangapandian; M Shekhar; P Mahinthichaichan; J L Baylon; T Jiang; Y Wang; M P Muller; E Shinn; Z Zhao; P-C Wen; E Tajkhorshid
Journal:  Methods Enzymol       Date:  2016-07-11       Impact factor: 1.600

3.  A fast and high-quality charge model for the next generation general AMBER force field.

Authors:  Xibing He; Viet H Man; Wei Yang; Tai-Sung Lee; Junmei Wang
Journal:  J Chem Phys       Date:  2020-09-21       Impact factor: 3.488

4.  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

5.  Toward Automated Benchmarking of Atomistic Force Fields: Neat Liquid Densities and Static Dielectric Constants from the ThermoML Data Archive.

Authors:  Kyle A Beauchamp; Julie M Behr; Ariën S Rustenburg; Christopher I Bayly; Kenneth Kroenlein; John D Chodera
Journal:  J Phys Chem B       Date:  2015-09-29       Impact factor: 2.991

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

Authors:  Guilherme Duarte Ramos Matos; Daisy Y Kyu; Hannes H Loeffler; John D Chodera; Michael R Shirts; David L Mobley
Journal:  J Chem Eng Data       Date:  2017-04-24       Impact factor: 2.694

Review 7.  An Empirical Polarizable Force Field Based on the Classical Drude Oscillator Model: Development History and Recent Applications.

Authors:  Justin A Lemkul; Jing Huang; Benoît Roux; Alexander D MacKerell
Journal:  Chem Rev       Date:  2016-01-27       Impact factor: 60.622

8.  Accuracy Test of the OPLS-AA Force Field for Calculating Free Energies of Mixing and Comparison with PAC-MAC.

Authors:  Augustinus J M Sweere; Johannes G E M Fraaije
Journal:  J Chem Theory Comput       Date:  2017-04-24       Impact factor: 6.006

9.  Evaluation of solvation free energies for small molecules with the AMOEBA polarizable force field.

Authors:  Noor Asidah Mohamed; Richard T Bradshaw; Jonathan W Essex
Journal:  J Comput Chem       Date:  2016-10-19       Impact factor: 3.376

10.  All-atom/coarse-grained hybrid predictions of distribution coefficients in SAMPL5.

Authors:  Samuel Genheden; Jonathan W Essex
Journal:  J Comput Aided Mol Des       Date:  2016-07-26       Impact factor: 3.686

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