Literature DB >> 19705172

Polarizability rescaling and atom-based Thole scaling in the CHARMM Drude polarizable force field for ethers.

Christopher M Baker1, Alexander D Mackerell.   

Abstract

Within the CHARMM polarizable force field based on the classical Drude oscillator, atomic polarizabilities are derived via fitting to ab initio calculated data on isolated gas phase molecules, with an empirical scaling factor applied to account for differences between the gas and condensed phases. In the development of polarizable models for the ethers, a polarizability scaling factor of 0.7 was previously applied [Vorobyov et al. J Comput Chem 3:1120-1133, 2007]. While the resulting force field models gave good agreement with a variety of experimental data, they systematically underestimated the liquid phase dielectric constants. Here, a new CHARMM polarizable model is developed for the ethers, employing a polarizability scaling factor of 0.85 and including atom-based Thole scale factors recently introduced into the CHARMM Drude polarizable force field [Harder et al. J Phys Chem B 112:3509-3521, 2008]. The new model offers a significant improvement in the reproduction of liquid phase dielectric constants, while maintaining the good agreement of the previous model with all other experimental and quantum mechanical data, highlighting the sensitivity of liquid phase properties to the choice of atomic polarizability parameters.

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Year:  2009        PMID: 19705172      PMCID: PMC2818097          DOI: 10.1007/s00894-009-0572-4

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


  13 in total

Review 1.  Empirical force fields for biological macromolecules: overview and issues.

Authors:  Alexander D Mackerell
Journal:  J Comput Chem       Date:  2004-10       Impact factor: 3.376

2.  The polarizability of point-polarizable water models: density functional theory/molecular mechanics results.

Authors:  Bernhard Schropp; Paul Tavan
Journal:  J Phys Chem B       Date:  2008-01-17       Impact factor: 2.991

Review 3.  CHARMM: the biomolecular simulation program.

Authors:  B R Brooks; C L Brooks; A D Mackerell; L Nilsson; R J Petrella; B Roux; Y Won; G Archontis; C Bartels; S Boresch; A Caflisch; L Caves; Q Cui; A R Dinner; M Feig; S Fischer; J Gao; M Hodoscek; W Im; K Kuczera; T Lazaridis; J Ma; V Ovchinnikov; E Paci; R W Pastor; C B Post; J Z Pu; M Schaefer; B Tidor; R M Venable; H L Woodcock; X Wu; W Yang; D M York; M Karplus
Journal:  J Comput Chem       Date:  2009-07-30       Impact factor: 3.376

4.  Evaluation of the molecular polarizability using the IPPP-CLOPPA-INDO/S method. Application to molecules of biological interest.

Authors:  Edith Botek; Claudia Giribet; Martín Ruiz de Azúa; Ricardo Martín Negri; Delia Bernik
Journal:  J Phys Chem A       Date:  2008-07-02       Impact factor: 2.781

5.  Molecular dynamics study of hydration in ethanol-water mixtures using a polarizable force field.

Authors:  Sergei Yu Noskov; Guillaume Lamoureux; Benoît Roux
Journal:  J Phys Chem B       Date:  2005-04-14       Impact factor: 2.991

6.  Polarizable empirical force field for alkanes based on the classical Drude oscillator model.

Authors:  Igor V Vorobyov; Victor M Anisimov; Alexander D MacKerell
Journal:  J Phys Chem B       Date:  2005-10-13       Impact factor: 2.991

7.  Water polarizability in condensed phase: ab initio evaluation by cluster approach.

Authors:  Akihiro Morita
Journal:  J Comput Chem       Date:  2002-11-30       Impact factor: 3.376

8.  Polarizable empirical force field for nitrogen-containing heteroaromatic compounds based on the classical Drude oscillator.

Authors:  Pedro E M Lopes; Guillaume Lamoureux; Alexander D Mackerell
Journal:  J Comput Chem       Date:  2009-09       Impact factor: 3.376

9.  Revised charge equilibration potential for liquid alkanes.

Authors:  Joseph E Davis; G Lee Warren; Sandeep Patel
Journal:  J Phys Chem B       Date:  2008-06-21       Impact factor: 2.991

10.  Understanding the dielectric properties of liquid amides from a polarizable force field.

Authors:  Edward Harder; Victor M Anisimov; Troy Whitfield; Alexander D MacKerell; Benoît Roux
Journal:  J Phys Chem B       Date:  2008-02-27       Impact factor: 2.991

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  31 in total

1.  Matching of additive and polarizable force fields for multiscale condensed phase simulations.

Authors:  Christopher M Baker; Robert B Best
Journal:  J Chem Theory Comput       Date:  2013-06-11       Impact factor: 6.006

2.  Kirkwood-Buff analysis of aqueous N-methylacetamide and acetamide solutions modeled by the CHARMM additive and Drude polarizable force fields.

Authors:  Bin Lin; Pedro E M Lopes; Benoît Roux; Alexander D MacKerell
Journal:  J Chem Phys       Date:  2013-08-28       Impact factor: 3.488

Review 3.  Metal Ion Modeling Using Classical Mechanics.

Authors:  Pengfei Li; Kenneth M Merz
Journal:  Chem Rev       Date:  2017-01-03       Impact factor: 60.622

4.  Polarizable Force Field for Molecular Ions Based on the Classical Drude Oscillator.

Authors:  Fang-Yu Lin; Pedro E M Lopes; Edward Harder; Benoît Roux; Alexander D MacKerell
Journal:  J Chem Inf Model       Date:  2018-04-17       Impact factor: 4.956

5.  Ab initio parameterization of YFF1, a universal force field for drug-design applications.

Authors:  Olexandr Ya Yakovenko; Yvonne Y Li; Alexander A Oliferenko; Ganna M Vashchenko; Volodymyr G Bdzhola; Steven J M Jones
Journal:  J Mol Model       Date:  2011-05-12       Impact factor: 1.810

Review 6.  Force field development phase II: Relaxation of physics-based criteria… or inclusion of more rigorous physics into the representation of molecular energetics.

Authors:  A T Hagler
Journal:  J Comput Aided Mol Des       Date:  2018-11-30       Impact factor: 3.686

7.  Force Field for Peptides and Proteins based on the Classical Drude Oscillator.

Authors:  Pedro E M Lopes; Jing Huang; Jihyun Shim; Yun Luo; Hui Li; Benoît Roux; Alexander D Mackerell
Journal:  J Chem Theory Comput       Date:  2013-12-10       Impact factor: 6.006

8.  All-atom polarizable force field for DNA based on the classical Drude oscillator model.

Authors:  Alexey Savelyev; Alexander D MacKerell
Journal:  J Comput Chem       Date:  2014-04-18       Impact factor: 3.376

Review 9.  CHARMM additive and polarizable force fields for biophysics and computer-aided drug design.

Authors:  K Vanommeslaeghe; A D MacKerell
Journal:  Biochim Biophys Acta       Date:  2014-08-19

10.  Recent Developments and Applications of the CHARMM force fields.

Authors:  Xiao Zhu; Pedro E M Lopes; Alexander D Mackerell
Journal:  Wiley Interdiscip Rev Comput Mol Sci       Date:  2011-06-28
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