Literature DB >> 31743030

Charge Scaling Manifesto: A Way of Reconciling the Inherently Macroscopic and Microscopic Natures of Molecular Simulations.

Brian J Kirby1,2, Pavel Jungwirth3.   

Abstract

Electronic polarization effects play an important role in the interactions of charged species in biologically relevant aqueous solutions, such as those involving salt ions, proteins, nucleic acids, or phospholipid membranes. Explicit inclusion of electronic polarization in molecular modeling is tedious both from the point of view of force field parametrization and actual performance of the simulations. Therefore, the vast majority of biomolecular simulations is performed using nonpolarizable force fields, which can lead to artifacts such as dramatically overestimated ion pairing, particularly when polyvalent ions are involved. Here, we show that many of these issues can be remedied without extra computational costs by including electronic polarization in a mean field way via charge rescaling. We also lay the solid physical foundations of this approach and reconcile from this perspective the microscopic versus macroscopic natures of nonpolarizable force fields.

Year:  2019        PMID: 31743030     DOI: 10.1021/acs.jpclett.9b02652

Source DB:  PubMed          Journal:  J Phys Chem Lett        ISSN: 1948-7185            Impact factor:   6.475


  6 in total

1.  Role of water in the determination of protonation states of titratable residues.

Authors:  Syeda Rehana Zia
Journal:  J Mol Model       Date:  2021-01-31       Impact factor: 1.810

2.  Influence of effective polarization on ion and water interactions within a biomimetic nanopore.

Authors:  Linda X Phan; Charlotte I Lynch; Jason Crain; Mark S P Sansom; Stephen J Tucker
Journal:  Biophys J       Date:  2022-05-07       Impact factor: 3.699

3.  Water Nanoconfined in a Hydrophobic Pore: Molecular Dynamics Simulations of Transmembrane Protein 175 and the Influence of Water Models.

Authors:  Charlotte I Lynch; Gianni Klesse; Shanlin Rao; Stephen J Tucker; Mark S P Sansom
Journal:  ACS Nano       Date:  2021-11-16       Impact factor: 15.881

4.  Ionic Strength and Solution Composition Dictate the Adsorption of Cell-Penetrating Peptides onto Phosphatidylcholine Membranes.

Authors:  Man Thi Hong Nguyen; Denys Biriukov; Carmelo Tempra; Katarina Baxova; Hector Martinez-Seara; Hüseyin Evci; Vandana Singh; Radek Šachl; Martin Hof; Pavel Jungwirth; Matti Javanainen; Mario Vazdar
Journal:  Langmuir       Date:  2022-09-09       Impact factor: 4.331

5.  Role of Viscosity in Deviations from the Nernst-Einstein Relation.

Authors:  Yunqi Shao; Keisuke Shigenobu; Masayoshi Watanabe; Chao Zhang
Journal:  J Phys Chem B       Date:  2020-06-01       Impact factor: 2.991

6.  Rolling circle RNA synthesis catalyzed by RNA.

Authors:  Emil Laust Kristoffersen; Matthew Burman; Agnes Noy; Philipp Holliger
Journal:  Elife       Date:  2022-02-02       Impact factor: 8.713

  6 in total

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