Literature DB >> 20804181

An accurate prediction of hydration free energies by combination of molecular integral equations theory with structural descriptors.

Ekaterina L Ratkova1, Gennady N Chuev, Volodymyr P Sergiievskyi, Maxim V Fedorov.   

Abstract

In this work, we report a novel method for the estimation of the hydration free energy of organic molecules, the structural descriptors correction (SDC) model. The method is based on a combination of the reference interaction site model (RISM) with several empirical corrections. The model requires only a small number of chemical descriptors associated with the main features of the chemical structure of solutes: excluded volume, branch, double bond, benzene ring, hydroxyl group, halogen atom, aldehyde group, ketone group, ether group, and phenol fragment. The optimum model was selected after testing of different RISM free energy expressions on a training set of 65 molecules. We show that the correction parameters of the SDC model are transferable between different chemical classes, which allows one to cover a wide range of organic solutes. The new model substantially increases the accuracy of calculated HFEs by RISM giving the standard deviation of the error for a test set of 120 organic molecules around 1.2 kcal/mol.

Entities:  

Year:  2010        PMID: 20804181     DOI: 10.1021/jp103955r

Source DB:  PubMed          Journal:  J Phys Chem B        ISSN: 1520-5207            Impact factor:   2.991


  8 in total

1.  Parameter optimization in differential geometry based solvation models.

Authors:  Bao Wang; G W Wei
Journal:  J Chem Phys       Date:  2015-10-07       Impact factor: 3.488

2.  A 3D-RISM/RISM study of the oseltamivir binding efficiency with the wild-type and resistance-associated mutant forms of the viral influenza B neuraminidase.

Authors:  Jiraphorn Phanich; Thanyada Rungrotmongkol; Daniel Sindhikara; Saree Phongphanphanee; Norio Yoshida; Fumio Hirata; Nawee Kungwan; Supot Hannongbua
Journal:  Protein Sci       Date:  2015-06-22       Impact factor: 6.725

3.  Variational approach for nonpolar solvation analysis.

Authors:  Zhan Chen; Shan Zhao; Jaehun Chun; Dennis G Thomas; Nathan A Baker; Peter W Bates; G W Wei
Journal:  J Chem Phys       Date:  2012-08-28       Impact factor: 3.488

4.  New theoretical method for rapid prediction of solvation free energy in water.

Authors:  Shuangliang Zhao; Zhehui Jin; Jianzhong Wu
Journal:  J Phys Chem B       Date:  2011-05-10       Impact factor: 2.991

5.  Simple electrolyte solutions: comparison of DRISM and molecular dynamics results for alkali halide solutions.

Authors:  In Suk Joung; Tyler Luchko; David A Case
Journal:  J Chem Phys       Date:  2013-01-28       Impact factor: 3.488

6.  Continuum Electrostatic Behavior of a 3D-RISM Theory.

Authors:  Benoît Roux
Journal:  J Phys Chem B       Date:  2020-08-17       Impact factor: 2.991

7.  Implementation and Optimization of the Embedded Cluster Reference Interaction Site Model with Atomic Charges.

Authors:  Ádám Ganyecz; Mihály Kállay
Journal:  J Phys Chem A       Date:  2022-04-08       Impact factor: 2.944

8.  Determining the hydration free energies of selected small molecules with MP2 and local MP2 through adaptive force matching.

Authors:  Dong Zheng; Ying Yuan; Feng Wang
Journal:  J Chem Phys       Date:  2021-03-14       Impact factor: 3.488

  8 in total

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