Literature DB >> 30830778

Ion-Hydroxyl Interactions: From High-Level Quantum Benchmarks to Transferable Polarizable Force Fields.

Vered Wineman-Fisher1, Yasmine Al-Hamdani2, Iqbal Addou1, Alexandre Tkatchenko2, Sameer Varma1.   

Abstract

Ion descriptors in molecular mechanics models are calibrated against reference data on ion-water interactions. It is then typically assumed that these descriptors will also satisfactorily describe interactions of ions with other functional groups, such as those present in biomolecules. However, several studies now demonstrate that this transferability assumption produces, in many different cases, large errors. Here we address this issue in a representative polarizable model and focus on transferability of cationic interactions from water to a series of alcohols. Both water and alcohols use hydroxyls for ion-coordination, and, therefore, this set of molecules constitutes the simplest possible case of transferability. We obtain gas phase reference data systematically from "gold-standard" quantum Monte Carlo and CCSD(T) methods, followed by benchmarked vdW-corrected DFT. We learn that the original polarizable model yields large gas phase wateralcohol transferability errors - the RMS and maximum errors are 2.3 and 5.1 kcal/mol, respectively. These errors are, nevertheless, systematic in that ion-alcohol interactions are overstabilized, and systematic errors typically imply that some essential physics is either missing or misrepresented. A comprehensive analysis shows that when both low- and high-field responses of ligand dipole polarization are described accurately, then transferability improves significantly - the RMS and maximum errors in the gas phase reduce, respectively, to 0.9 and 2.5 kcal/mol. Additionally, predictions of condensed phase transfer free energies also improve. Nevertheless, within the limits of the extrathermodynamic assumptions necessary to separate experimental estimates of salt dissolution into constituent cationic and anionic contributions, we note that the error in the condensed phase is systematic, which we attribute, at least, partially to the parametrization in long-range electrostatics. Overall, this work demonstrates a rational approach to boosting transferability of ionic interactions that will be applicable broadly to improving other polarizable and nonpolarizable models.

Entities:  

Year:  2019        PMID: 30830778      PMCID: PMC6598712          DOI: 10.1021/acs.jctc.8b01198

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


  47 in total

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Authors:  Alan Grossfield; Pengyu Ren; Jay W Ponder
Journal:  J Am Chem Soc       Date:  2003-12-17       Impact factor: 15.419

Review 2.  Molecular dynamics simulations of biomolecules.

Authors:  Martin Karplus; J Andrew McCammon
Journal:  Nat Struct Biol       Date:  2002-09

3.  Smooth relativistic Hartree-Fock pseudopotentials for H to Ba and Lu to Hg.

Authors:  J R Trail; R J Needs
Journal:  J Chem Phys       Date:  2005-05-01       Impact factor: 3.488

4.  Accurate Coulomb-fitting basis sets for H to Rn.

Authors:  Florian Weigend
Journal:  Phys Chem Chem Phys       Date:  2006-01-03       Impact factor: 3.676

Review 5.  Coordination numbers of alkali metal ions in aqueous solutions.

Authors:  Sameer Varma; Susan B Rempe
Journal:  Biophys Chem       Date:  2006-07-27       Impact factor: 2.352

6.  Canonical sampling through velocity rescaling.

Authors:  Giovanni Bussi; Davide Donadio; Michele Parrinello
Journal:  J Chem Phys       Date:  2007-01-07       Impact factor: 3.488

7.  Towards accurate solvation dynamics of divalent cations in water using the polarizable amoeba force field: From energetics to structure.

Authors:  Jean-Philip Piquemal; Lalith Perera; G Andrés Cisneros; Pengyu Ren; Lee G Pedersen; Thomas A Darden
Journal:  J Chem Phys       Date:  2006-08-07       Impact factor: 3.488

Review 8.  Role of Na+ and K+ in enzyme function.

Authors:  Michael J Page; Enrico Di Cera
Journal:  Physiol Rev       Date:  2006-10       Impact factor: 37.312

9.  Many-body potentials for aqueous Li(+), Na(+), Mg(2+), and Al(3+): comparison of effective three-body potentials and polarizable models.

Authors:  Daniel Spångberg; Kersti Hermansson
Journal:  J Chem Phys       Date:  2004-03-08       Impact factor: 3.488

10.  Absolute hydration free energy scale for alkali and halide ions established from simulations with a polarizable force field.

Authors:  Guillaume Lamoureux; Benoît Roux
Journal:  J Phys Chem B       Date:  2006-02-23       Impact factor: 2.991

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  2 in total

1.  Transferable interactions of Li+ and Mg2+ ions in polarizable models.

Authors:  Vered Wineman-Fisher; Julián Meléndez Delgado; Péter R Nagy; Eric Jakobsson; Sagar A Pandit; Sameer Varma
Journal:  J Chem Phys       Date:  2020-09-14       Impact factor: 3.488

2.  Molecular basis for higher affinity of SARS-CoV-2 spike RBD for human ACE2 receptor.

Authors:  Julián M Delgado; Nalvi Duro; David M Rogers; Alexandre Tkatchenko; Sagar A Pandit; Sameer Varma
Journal:  Proteins       Date:  2021-04-26
  2 in total

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