Literature DB >> 18802495

Polarizable empirical force field for the primary and secondary alcohol series based on the classical Drude model.

Victor M Anisimov1, Igor V Vorobyov, Benoît Roux, Alexander D Mackerell.   

Abstract

A polarizable empirical force field based on the classical Drude oscillator has been developed for the aliphatic alcohol series. The model is optimized with emphasis on condensed-phase properties and is validated against a variety of experimental data. Transferability of the developed parameters is emphasized by the use of a single electrostatic model for the hydroxyl group throughout the alcohol series. Aliphatic moiety parameters were transferred from the polarizable alkane parameter set, with only the Lennard-Jones parameters on the carbon in methanol optimized. The developed model yields good agreement with pure solvent properties with the exception of the heats of vaporization of 1-propanol and 1-butanol, which are underestimated by approximately 6%; special LJ parameters for the oxygen in these two molecules that correct for this limitation are presented. Accurate treatment of the free energies of aqueous solvation required the use of atom-type specific O(alcohol)-O(water) LJ interaction terms, with specific terms used for the primary and secondary alcohols. With respect to gas phase properties the polarizable model overestimates experimental dipole moments and quantum mechanical interaction energies with water by approximately 10 and 8 %, respectively, a significant improvement over 44 and 46 % overestimations of the corresponding properties in the CHARMM22 fixed-charge additive model. Comparison of structural properties of the polarizable and additive models for the pure solvents and in aqueous solution shows significant differences indicating atomic details of intermolecular interactions to be sensitive to the applied force field. The polarizable model predicts pure solvent and aqueous phase dipole moment distributions for ethanol centered at 2.4 and 2.7 D, respectively, a significant increase over the gas phase value of 1.8 D, whereas in a solvent of lower polarity, benzene, a value of 1.9 is obtained. The ability of the polarizable model to yield changes in dipole moment as well as the reproduction of a range of condensed phase properties indicates its utility in the study of the properties of alcohols in a variety of condensed phase environments as well as representing an important step in the development of a comprehensive force field for biological molecules.

Entities:  

Year:  2007        PMID: 18802495      PMCID: PMC2542883          DOI: 10.1021/ct700100a

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


  17 in total

1.  CHARMM fluctuating charge force field for proteins: II protein/solvent properties from molecular dynamics simulations using a nonadditive electrostatic model.

Authors:  Sandeep Patel; Alexander D Mackerell; Charles L Brooks
Journal:  J Comput Chem       Date:  2004-09       Impact factor: 3.376

Review 2.  Empirical force fields for biological macromolecules: overview and issues.

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

3.  A generating equation for mixing rules and two new mixing rules for interatomic potential energy parameters.

Authors:  Ali Khalaf Al-Matar; David A Rockstraw
Journal:  J Comput Chem       Date:  2004-04-15       Impact factor: 3.376

4.  A nonadditive methanol force field: bulk liquid and liquid-vapor interfacial properties via molecular dynamics simulations using a fluctuating charge model.

Authors:  Sandeep Patel; Charles L Brooks
Journal:  J Chem Phys       Date:  2005-01-08       Impact factor: 3.488

5.  Structure, thermodynamics, and liquid-vapor equilibrium of ethanol from molecular-dynamics simulations using nonadditive interactions.

Authors:  Sandeep Patel; Charles L Brooks
Journal:  J Chem Phys       Date:  2005-10-22       Impact factor: 3.488

6.  An ab initio study on the torsional surface of alkanes and its effect on molecular simulations of alkanes and a DPPC bilayer.

Authors:  Jeffery B Klauda; Bernard R Brooks; Alexander D MacKerell; Richard M Venable; Richard W Pastor
Journal:  J Phys Chem B       Date:  2005-03-24       Impact factor: 2.991

7.  Molecular dynamics simulations of liquid methanol and methanol-water mixtures with polarizable models.

Authors:  Haibo Yu; Daan P Geerke; Haiyan Liu; Wilfred F van Gunsteren
Journal:  J Comput Chem       Date:  2006-10       Impact factor: 3.376

8.  Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density.

Authors: 
Journal:  Phys Rev B Condens Matter       Date:  1988-01-15

9.  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

10.  Alcohols, ethers, carbohydrates, and related compounds. I. The MM4 force field for simple compounds.

Authors:  Norman L Allinger; Kuo-Hsiang Chen; Jenn-Huei Lii; Kathleen A Durkin
Journal:  J Comput Chem       Date:  2003-09       Impact factor: 3.376

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  64 in total

1.  Toward Learned Chemical Perception of Force Field Typing Rules.

Authors:  Camila Zanette; Caitlin C Bannan; Christopher I Bayly; Josh Fass; Michael K Gilson; Michael R Shirts; John D Chodera; David L Mobley
Journal:  J Chem Theory Comput       Date:  2018-12-24       Impact factor: 6.006

2.  Polarizable force field for RNA based on the classical drude oscillator.

Authors:  Justin A Lemkul; Alexander D MacKerell
Journal:  J Comput Chem       Date:  2018-12-15       Impact factor: 3.376

3.  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

4.  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

5.  Opening and closing of the periplasmic gate in lactose permease.

Authors:  Yonggang Zhou; Lan Guan; J Alfredo Freites; H Ronald Kaback
Journal:  Proc Natl Acad Sci U S A       Date:  2008-03-04       Impact factor: 11.205

Review 6.  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

7.  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

8.  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 9.  Classical electrostatics for biomolecular simulations.

Authors:  G Andrés Cisneros; Mikko Karttunen; Pengyu Ren; Celeste Sagui
Journal:  Chem Rev       Date:  2013-08-27       Impact factor: 60.622

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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