Literature DB >> 27585395

A Seamless Grid-Based Interface for Mean-Field QM/MM Coupled with Efficient Solvation Free Energy Calculations.

Hyung-Kyu Lim1, Hankyul Lee1, Hyungjun Kim1.   

Abstract

Among various models that incorporate solvation effects into first-principles-based electronic structure theory such as density functional theory (DFT), the average solvent electrostatic potential/molecular dynamics (ASEP/MD) method is particularly advantageous. This method explicitly includes the nature of complicated solvent structures that is absent in implicit solvation methods. Because the ASEP/MD method treats only solvent molecule dynamics, it requires less computational cost than the conventional quantum mechanics/molecular mechanics (QM/MM) approaches. Herein, we present a real-space rectangular grid-based method to implement the mean-field QM/MM idea of ASEP/MD to plane-wave DFT, which is termed "DFT in classical explicit solvents", or DFT-CES. By employing a three-dimensional real-space grid as a communication medium, we can treat the electrostatic interactions between the DFT solute and the ASEP sampled from MD simulations in a seamless and straightforward manner. Moreover, we couple a fast and efficient free energy calculation method based on the two-phase thermodynamic (2PT) model with our DFT-CES method, which enables direct and simultaneous computation of the solvation free energies as well as the geometric and electronic responses of a solute of interest under the solvation effect. With the aid of DFT-CES/2PT, we investigate the solvation free energies and detailed solvation thermodynamics for 17 types of organic molecules, which show good agreement with the experimental data. We further compare our simulation results with previous theoretical models and assumptions made for the development of implicit solvation models. We anticipate that our proposed method, DFT-CES/2PT, will enable vast utilization of the ASEP/MD method for investigating solvation properties of materials by using periodic DFT calculations in the future.

Entities:  

Year:  2016        PMID: 27585395     DOI: 10.1021/acs.jctc.6b00469

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


  7 in total

1.  Solvation Free Energy Calculations with Quantum Mechanics/Molecular Mechanics and Machine Learning Models.

Authors:  Pan Zhang; Lin Shen; Weitao Yang
Journal:  J Phys Chem B       Date:  2019-01-15       Impact factor: 2.991

Review 2.  Implicit Solvation Methods for Catalysis at Electrified Interfaces.

Authors:  Stefan Ringe; Nicolas G Hörmann; Harald Oberhofer; Karsten Reuter
Journal:  Chem Rev       Date:  2021-12-20       Impact factor: 72.087

3.  Hydration Thermodynamics of Non-Polar Aromatic Hydrocarbons: Comparison of Implicit and Explicit Solvation Models.

Authors:  Hankyul Lee; Hyung-Kyu Lim; Hyungjun Kim
Journal:  Molecules       Date:  2018-11-09       Impact factor: 4.411

4.  Structure, Dynamics, and Wettability of Water at Metal Interfaces.

Authors:  Suji Gim; Kang Jin Cho; Hyung-Kyu Lim; Hyungjun Kim
Journal:  Sci Rep       Date:  2019-10-15       Impact factor: 4.379

5.  On the importance of the electric double layer structure in aqueous electrocatalysis.

Authors:  Seung-Jae Shin; Dong Hyun Kim; Geunsu Bae; Stefan Ringe; Hansol Choi; Hyung-Kyu Lim; Chang Hyuck Choi; Hyungjun Kim
Journal:  Nat Commun       Date:  2022-01-10       Impact factor: 17.694

6.  A unifying mechanism for cation effect modulating C1 and C2 productions from CO2 electroreduction.

Authors:  Seung-Jae Shin; Hansol Choi; Stefan Ringe; Da Hye Won; Hyung-Suk Oh; Dong Hyun Kim; Taemin Lee; Dae-Hyun Nam; Hyungjun Kim; Chang Hyuck Choi
Journal:  Nat Commun       Date:  2022-09-19       Impact factor: 17.694

7.  Thermodynamics of π-π Interactions of Benzene and Phenol in Water.

Authors:  Dooam Paik; Hankyul Lee; Hyungjun Kim; Jeong-Mo Choi
Journal:  Int J Mol Sci       Date:  2022-08-29       Impact factor: 6.208

  7 in total

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