Literature DB >> 32447472

Balanced polarizable Drude force field parameters for molecular anions: phosphates, sulfates, sulfamates, and oxides.

Abhishek A Kognole1, Asaminew H Aytenfisu1, Alexander D MacKerell2.   

Abstract

Polarizable force fields are emerging as a more accurate alternative to additive force fields in terms of modeling and simulations of a variety of chemicals including biomolecules. Explicit treatment of induced polarization in charged species such as phosphates and sulfates offers the potential for achieving an improved atomistic understanding of the physical forces driving their interactions with their environments. To help achieve this, in this study we present balanced Drude polarizable force field parameters for molecular ions including phosphates, sulfates, sulfamates, and oxides. Better balance was primarily achieved in the relative values of minimum interaction energies and distances of the anionic model compounds with water at the Drude and quantum mechanical (QM) model chemistries. Parametrization involved reoptimizing available parameters as well as extending the force field to new molecules with the goal of achieving self-consistency with respect to the Lennard-Jones and electrostatic parameters targeting QM and experimental hydration free energies. The resulting force field parameters achieve consistent treatment across the studied anions, facilitating more balanced simulations of biomolecules and small organic molecules in the context of the classical Drude polarizable force field. Graphical abstract.

Entities:  

Keywords:  CHARMM; Molecular dynamics; Molecular ions; Molecular modeling; Polarizable force field

Year:  2020        PMID: 32447472      PMCID: PMC7326346          DOI: 10.1007/s00894-020-04399-0

Source DB:  PubMed          Journal:  J Mol Model        ISSN: 0948-5023            Impact factor:   1.810


  74 in total

1.  Polarizable force field for RNA based on the classical drude oscillator.

Authors:  Justin A Lemkul; Alexander D MacKerell
Journal:  J Comput Chem       Date:  2018-12-15       Impact factor: 3.376

2.  Determination of Electrostatic Parameters for a Polarizable Force Field Based on the Classical Drude Oscillator.

Authors:  Victor M Anisimov; Guillaume Lamoureux; Igor V Vorobyov; Niu Huang; Benoît Roux; Alexander D MacKerell
Journal:  J Chem Theory Comput       Date:  2005-01       Impact factor: 6.006

Review 3.  Recent advances in molecular simulations of ion solvation at liquid interfaces.

Authors:  Tsun-Mei Chang; Liem X Dang
Journal:  Chem Rev       Date:  2006-04       Impact factor: 60.622

Review 4.  Specific ion effects at the air/water interface.

Authors:  Pavel Jungwirth; Douglas J Tobias
Journal:  Chem Rev       Date:  2006-04       Impact factor: 60.622

5.  "Squiggle-H2O". An enquiry into the importance of solvation effects in phosphate ester and anhydride reactions.

Authors:  P George; R J Witonsky; M Trachtman; C Wu; W Dorwart; L Richman; W Richman; F Shurayh; B Lentz
Journal:  Biochim Biophys Acta       Date:  1970-11-03

6.  Development of the CHARMM Force Field for Lipids.

Authors:  R W Pastor; A D Mackerell
Journal:  J Phys Chem Lett       Date:  2011       Impact factor: 6.475

7.  Polarizable Force Field for DNA Based on the Classical Drude Oscillator: I. Refinement Using Quantum Mechanical Base Stacking and Conformational Energetics.

Authors:  Justin A Lemkul; Alexander D MacKerell
Journal:  J Chem Theory Comput       Date:  2017-04-19       Impact factor: 6.006

8.  CHARMM fluctuating charge force field for proteins: I parameterization and application to bulk organic liquid simulations.

Authors:  Sandeep Patel; Charles L Brooks
Journal:  J Comput Chem       Date:  2004-01-15       Impact factor: 3.376

9.  SM6:  A Density Functional Theory Continuum Solvation Model for Calculating Aqueous Solvation Free Energies of Neutrals, Ions, and Solute-Water Clusters.

Authors:  Casey P Kelly; Christopher J Cramer; Donald G Truhlar
Journal:  J Chem Theory Comput       Date:  2005-11       Impact factor: 6.006

10.  Connecting the kinetics and energy landscape of tRNA translocation on the ribosome.

Authors:  Paul C Whitford; Scott C Blanchard; Jamie H D Cate; Karissa Y Sanbonmatsu
Journal:  PLoS Comput Biol       Date:  2013-03-21       Impact factor: 4.475

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  3 in total

1.  Extension of the CHARMM Classical Drude Polarizable Force Field to N- and O-Linked Glycopeptides and Glycoproteins.

Authors:  Abhishek A Kognole; Asaminew H Aytenfisu; Alexander D MacKerell
Journal:  J Phys Chem B       Date:  2022-08-25       Impact factor: 3.466

2.  Harnessing Deep Learning for Optimization of Lennard-Jones Parameters for the Polarizable Classical Drude Oscillator Force Field.

Authors:  Payal Chatterjee; Mert Y Sengul; Anmol Kumar; Alexander D MacKerell
Journal:  J Chem Theory Comput       Date:  2022-04-01       Impact factor: 6.578

3.  SAMPL7 Host-Guest Challenge Overview: assessing the reliability of polarizable and non-polarizable methods for binding free energy calculations.

Authors:  Martin Amezcua; Léa El Khoury; David L Mobley
Journal:  J Comput Aided Mol Des       Date:  2021-01-04       Impact factor: 3.686

  3 in total

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