Literature DB >> 26610135

Combination of RISM and Cheminformatics for Efficient Predictions of Hydration Free Energy of Polyfragment Molecules: Application to a Set of Organic Pollutants.

Ekaterina L Ratkova1, Maxim V Fedorov1.   

Abstract

Here, we discuss a new method for predicting the hydration free energy (HFE) of organic pollutants and illustrate the efficiency of the method on a set of 220 chlorinated aromatic hydrocarbons. The new model is computationally inexpensive, with one HFE calculation taking less than a minute on a PC. The method is based on a combination of a molecular integral equations theory, one-dimensional reference interaction site model (1D RISM), with the cheminformatics approach. We correct HFEs obtained by the 1D RISM with a set of empirical corrections. The corrections are associated with the partial molar volume and structural descriptors of the molecules. We show that the introduced corrections can significantly improve the quality of the 1D RISM HFE predictions obtained by the partial wave free energy expression [ Ten-no , S. J. Chem. Phys. 2001 , 115 , 3724 ] and the Kovalenko-Hirata closure [ Kovalenko , A. ; Hirata , F. J. Chem. Phys. 1999 , 110 , 10095 ]. We also show that the quality of the model can be further improved by the reparametrization using QM-derived partial charges instead of the originally used OPLS-AA partial charges. The final model gives good results for polychlorinated benzenes (the mean and standard deviation of the error are 0.02 and 0.36 kcal/mol, correspondingly). At the same time, the model gives somewhat worse results for polychlorobiphenyls (PCBs) with a systematic bias of -0.72 kcal/mol but a small standard deviation equal to 0.55 kcal/mol. We note that the error remains the same for the whole set of PCBs, whereas errors of HFEs predicted with continuum solvation models (data were taken from Phillips , K. L. et al. Environ. Sci. Technol. 2008 , 42 , 8412 ) increase significantly for higher chlorinated PCB congeners. In conclusion, we discuss potential future applications of the model and several avenues for its further improvement.

Entities:  

Year:  2011        PMID: 26610135     DOI: 10.1021/ct100654h

Source DB:  PubMed          Journal:  J Chem Theory Comput        ISSN: 1549-9618            Impact factor:   6.006


  4 in total

1.  Predicting hydration free energies of polychlorinated aromatic compounds from the SAMPL-3 data set with FiSH and LIE models.

Authors:  Traian Sulea; Enrico O Purisima
Journal:  J Comput Aided Mol Des       Date:  2011-12-22       Impact factor: 3.686

2.  Prediction of hydration free energies for aliphatic and aromatic chloro derivatives using molecular dynamics simulations with the OPLS-AA force field.

Authors:  Oliver Beckstein; Bogdan I Iorga
Journal:  J Comput Aided Mol Des       Date:  2011-12-21       Impact factor: 3.686

3.  Comparing Alchemical Free Energy Estimates to Experimental Values Based on the Ben-Naim Formula: How Much Agreement Can We Expect?

Authors:  T Ryan Rogers; Feng Wang
Journal:  J Phys Chem B       Date:  2020-01-23       Impact factor: 2.991

4.  Uniting cheminformatics and chemical theory to predict the intrinsic aqueous solubility of crystalline druglike molecules.

Authors:  James L McDonagh; Neetika Nath; Luna De Ferrari; Tanja van Mourik; John B O Mitchell
Journal:  J Chem Inf Model       Date:  2014-03-11       Impact factor: 4.956

  4 in total

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