Literature DB >> 23703219

Polarizable empirical force field for acyclic polyalcohols based on the classical Drude oscillator.

Xibing He1, Pedro E M Lopes, Alexander D Mackerell.   

Abstract

A polarizable empirical force field for acyclic polyalcohols based on the classical Drude oscillator is presented. The model is optimized with an emphasis on the transferability of the developed parameters among molecules of different sizes in this series and on the condensed-phase properties validated against experimental data. The importance of the explicit treatment of electronic polarizability in empirical force fields is demonstrated in the cases of this series of molecules with vicinal hydroxyl groups that can form cooperative intra- and intermolecular hydrogen bonds. Compared to the CHARMM additive force field, improved treatment of the electrostatic interactions avoids overestimation of the gas-phase dipole moments resulting in significant improvement in the treatment of the conformational energies and leads to the correct balance of intra- and intermolecular hydrogen bonding of glycerol as evidenced by calculated heat of vaporization being in excellent agreement with experiment. Computed condensed phase data, including crystal lattice parameters and volumes and densities of aqueous solutions are in better agreement with experimental data as compared to the corresponding additive model. Such improvements are anticipated to significantly improve the treatment of polymers in general, including biological macromolecules.
Copyright © 2013 Wiley Periodicals, Inc.

Entities:  

Keywords:  1,2-ethanediol; CHARMM polarizable force field; carbohydrate; ethylene glycol; glycerol; molecular dynamics simulation; monosaccharide; polyols

Mesh:

Substances:

Year:  2013        PMID: 23703219      PMCID: PMC3902549          DOI: 10.1002/bip.22286

Source DB:  PubMed          Journal:  Biopolymers        ISSN: 0006-3525            Impact factor:   2.505


  84 in total

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5.  Hydration properties of xylitol: computer simulation.

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6.  Molecular dynamics study of effects of temperature and concentration on hydrogen-bond abilities of ethylene glycol and glycerol: implications for cryopreservation.

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9.  Hydrogen bonding and the cryoprotective properties of glycerol/water mixtures.

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Journal:  J Phys Chem B       Date:  2006-07-13       Impact factor: 2.991

10.  Additive and Classical Drude Polarizable Force Fields for Linear and Cyclic Ethers.

Authors:  Igor Vorobyov; Victor M Anisimov; Shannon Greene; Richard M Venable; Adam Moser; Richard W Pastor; Alexander D MacKerell
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  23 in total

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

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2.  Drude polarizable force field for aliphatic ketones and aldehydes, and their associated acyclic carbohydrates.

Authors:  Meagan C Small; Asaminew H Aytenfisu; Fang-Yu Lin; Xibing He; Alexander D MacKerell
Journal:  J Comput Aided Mol Des       Date:  2017-02-11       Impact factor: 3.686

3.  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

4.  Drude Polarizable Force Field for Molecular Dynamics Simulations of Saturated and Unsaturated Zwitterionic Lipids.

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Journal:  J Chem Theory Comput       Date:  2017-08-08       Impact factor: 6.006

Review 5.  Force field development phase II: Relaxation of physics-based criteria… or inclusion of more rigorous physics into the representation of molecular energetics.

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

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

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8.  Proper balance of solvent-solute and solute-solute interactions in the treatment of the diffusion of glucose using the Drude polarizable force field.

Authors:  Mingjun Yang; Asaminew H Aytenfisu; Alexander D MacKerell
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Review 9.  CHARMM additive and polarizable force fields for biophysics and computer-aided drug design.

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10.  Further Optimization and Validation of the Classical Drude Polarizable Protein Force Field.

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