Literature DB >> 26627431

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

Igor Vorobyov1, Victor M Anisimov1, Shannon Greene1, Richard M Venable1, Adam Moser1, Richard W Pastor1, Alexander D MacKerell1.   

Abstract

Empirical force field parameters consistent with the CHARMM additive and classical Drude based polarizable force fields are presented for linear and cyclic ethers. Initiation of the optimization process involved validation of the aliphatic parameters based on linear alkanes and cyclic alkanes. Results showed the transfer to cyclohexane to yield satisfactory agreement with target data; however, in the case of cyclopentane direct transfer of the Lennard-Jones parameters was not sufficient due to ring strain, requiring additional optimization of these parameters for this molecule. Parameters for the ethers were then developed starting with the available aliphatic parameters, with the nonbond parameters for the oxygens optimized to reproduce both gas- and condensed-phase properties. Nonbond parameters for the polarizable model include the use of an anisotropic electrostatic model on the oxygens. Parameter optimization emphasized the development of transferable parameters between the ethers of a given class. The ether models are shown to be in satisfactory agreement with both pure solvent and aqueous solvation properties, and the resulting parameters are transferable to test molecules. The presented force field will allow for simulation studies of ethers in condensed phase and provides a basis for ongoing developments in both additive and polarizable force fields for biological molecules.

Entities:  

Year:  2007        PMID: 26627431     DOI: 10.1021/ct600350s

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


  60 in total

1.  Electronic continuum model for molecular dynamics simulations of biological molecules.

Authors:  I V Leontyev; A A Stuchebrukhov
Journal:  J Chem Theory Comput       Date:  2010       Impact factor: 6.006

2.  CHARMM additive all-atom force field for carbohydrate derivatives and its utility in polysaccharide and carbohydrate-protein modeling.

Authors:  Olgun Guvench; Sairam S Mallajosyula; E Prabhu Raman; Elizabeth Hatcher; Kenno Vanommeslaeghe; Theresa J Foster; Francis W Jamison; Alexander D Mackerell
Journal:  J Chem Theory Comput       Date:  2011-10-11       Impact factor: 6.006

3.  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

4.  The Surface of Protein λ6-85 Can Act as a Template for Recurring Poly(ethylene glycol) Structure.

Authors:  Shu-Han Chao; Jan Schäfer; Martin Gruebele
Journal:  Biochemistry       Date:  2017-10-06       Impact factor: 3.162

5.  Electronic continuum model for molecular dynamics simulations.

Authors:  I V Leontyev; A A Stuchebrukhov
Journal:  J Chem Phys       Date:  2009-02-28       Impact factor: 3.488

6.  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

7.  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

Review 8.  Metal Ion Modeling Using Classical Mechanics.

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

9.  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

10.  Automated conformational energy fitting for force-field development.

Authors:  Olgun Guvench; Alexander D MacKerell
Journal:  J Mol Model       Date:  2008-05-06       Impact factor: 1.810

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