Evidence map›Paper›PMID 39670846›Full record

ArticleJournal of chemical theory and computation2024

From Implicit to Explicit: An Interaction-Reorganization Approach to Molecular Solvation Energy.

Kaifang Huang, Lili Duan, John Z H Zhang

Abstract read
In one paragraph

Article in Journal of chemical theory and computation, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

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2 · The registry

The trial behind it

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3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. Review
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

3 authors.

Kaifang HuangShanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Key Laboratory of Green Chemistry & Chemical Process, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China.
Lili DuanSchool of Physics and Electronics, Shandong Normal University, Jinan, 250014, China.
John Z H ZhangShanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Key Laboratory of Green Chemistry & Chemical Process, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Accurate calculation of solvation energies has long fascinated researchers, but complex interactions within bulk water molecules pose significant challenges. Currently, molecular solvation energy calculations are mostly based on implicit solvent approximations in which the solvent molecules are treated as continuum dielectric media. However, the implicit solvent approach is not ideal because it lacks certain real solvation effects, such as that of the first solvation shell, etc. Here, we propose an explicit solvent approach, interaction-reorganization solvation (IRS) method, for molecular solvation energy calculations. The IRS approach achieves predictive accuracy comparable to that of the widely recognized solvation model based on the density (SMD) method and is significantly more accurate than that of the Poisson-Boltzmann/generalized Born surface area (PB/GBSA) methods. This is demonstrated in both the correlation coefficient and the mean absolute error (MAE) with respect to the experimental data. The IRS method is based on molecular dynamics simulation in explicit solvent and does not need to solve Poisson-Boltzmann or Schrödinger equations. On the other hand, the accuracy of the IRS method does depend on the accuracy of the molecular force field used in MD simulations. We expect that the IRS method will be very useful for the solvation energy calculations of molecules.

Identifiers

PMID39670846
PMCPMC11674157

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.