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  Developing force fields when experimental data is sparse: AMBER/GAFF-compatible parameters for inorganic and alkyl oxoanions

Kashefolgheta, S., & Vila Verde, A. (2017). Developing force fields when experimental data is sparse: AMBER/GAFF-compatible parameters for inorganic and alkyl oxoanions. Physical Chemistry Chemical Physics, 19(31), 20593-20607. doi:10.1039/C7CP02557B.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-002D-A303-D Version Permalink: http://hdl.handle.net/21.11116/0000-0002-9D69-8
Genre: Journal Article

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 Creators:
Kashefolgheta, S.1, Author              
Vila Verde, Ana1, Author              
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1Ana Vila Verde, Theorie & Bio-Systeme, Max Planck Institute of Colloids and Interfaces, Max Planck Society, ou_2205638              

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 Dates: 2017-07-172017-08-21
 Publication Status: Published in print
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 Table of Contents: We present a set of Lennard-Jones parameters for classical, all-atom models of acetate and various alkylated and non-alkylated forms of sulfate, sulfonate and phosphate ions, optimized to reproduce their interactions with water and with the physiologically relevant sodium, ammonium and methylammonium cations. The parameters are internally consistent and are fully compatible with the Generalized Amber Force Field (GAFF), the AMBER force field for proteins, the accompanying TIP3P water model and the sodium model of Joung and Cheatham. The parameters were developed primarily relying on experimental information – hydration free energies and solution activity derivatives at 0.5 m concentration – with ab initio, gas phase calculations being used for the cases where experimental information is missing. The ab initio parameterization scheme presented here is distinct from other approaches because it explicitly connects gas phase binding energies to intermolecular interactions in solution. We demonstrate that the original GAFF/AMBER parameters often overestimate anion–cation interactions, leading to an excessive number of contact ion pairs in solutions of carboxylate ions, and to aggregation in solutions of divalent ions. GAFF/AMBER parameters lead to excessive numbers of salt bridges in proteins and of contact ion pairs between sodium and acidic protein groups, issues that are resolved by using the optimized parameters presented here.
 Rev. Method: Peer
 Identifiers: DOI: 10.1039/C7CP02557B
DOI: 10.1039/C8CP91863E
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Title: Physical Chemistry Chemical Physics
  Abbreviation : Phys. Chem. Chem. Phys.
Source Genre: Journal
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Publ. Info: Cambridge, England : Royal Society of Chemistry
Pages: - Volume / Issue: 19 (31) Sequence Number: - Start / End Page: 20593 - 20607 Identifier: ISSN: 1463-9076

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Title: Physical Chemistry Chemical Physics
  Abbreviation : Phys. Chem. Chem. Phys.
Source Genre: Journal
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Publ. Info: Cambridge, England : Royal Society of Chemistry
Pages: - Volume / Issue: 20 (44) Sequence Number: - Start / End Page: 28346 - 28347 Identifier: ISSN: 1463-9076