Literature DB >> 23947568

A comparative Kirkwood-Buff study of aqueous methanol solutions modeled by the CHARMM additive and Drude polarizable force fields.

Bin Lin1, Xibing He, Alexander D MacKerell.   

Abstract

A comparative study on aqueous methanol solutions modeled by the CHARMM additive and Drude polarizable force fields was carried out by employing Kirkwood-Buff analysis. It was shown that both models reproduced the experimental Kirkwood-Buff integrals and excess coordination numbers adequately well over the entire concentration range. The Drude model showed significant improvement over the additive model in solution densities, partial molar volumes, excess molar volumes, concentration-dependent diffusion constants, and dielectric constants. However, the additive model performed somewhat better than the Drude model in reproducing the activity derivative, excess molar Gibbs energy, and excess molar enthalpy of mixing. This is due to the additive achieving a better balance among solute-solute, solute-solvent, and solvent-solvent interactions, indicating the potential for improvements in the Drude polarizable alcohol model.

Entities:  

Mesh:

Substances:

Year:  2013        PMID: 23947568      PMCID: PMC3787518          DOI: 10.1021/jp4061889

Source DB:  PubMed          Journal:  J Phys Chem B        ISSN: 1520-5207            Impact factor:   2.991


  30 in total

Review 1.  Force fields for protein simulations.

Authors:  Jay W Ponder; David A Case
Journal:  Adv Protein Chem       Date:  2003

2.  Polarizable Force Fields:  History, Test Cases, and Prospects.

Authors:  Arieh Warshel; Mitsunori Kato; Andrei V Pisliakov
Journal:  J Chem Theory Comput       Date:  2007-11       Impact factor: 6.006

3.  The GROMOS software for biomolecular simulation: GROMOS05.

Authors:  Markus Christen; Philippe H Hünenberger; Dirk Bakowies; Riccardo Baron; Roland Bürgi; Daan P Geerke; Tim N Heinz; Mika A Kastenholz; Vincent Kräutler; Chris Oostenbrink; Christine Peter; Daniel Trzesniak; Wilfred F van Gunsteren
Journal:  J Comput Chem       Date:  2005-12       Impact factor: 3.376

Review 4.  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

5.  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
Journal:  J Chem Theory Comput       Date:  2007-05       Impact factor: 6.006

6.  The Origin of Layer Structure Artifacts in Simulations of Liquid Water.

Authors:  David van der Spoel; Paul J van Maaren
Journal:  J Chem Theory Comput       Date:  2006-01       Impact factor: 6.006

7.  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

8.  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

9.  CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields.

Authors:  K Vanommeslaeghe; E Hatcher; C Acharya; S Kundu; S Zhong; J Shim; E Darian; O Guvench; P Lopes; I Vorobyov; A D Mackerell
Journal:  J Comput Chem       Date:  2010-03       Impact factor: 3.376

Review 10.  Ion selectivity in channels and transporters.

Authors:  Benoît Roux; Simon Bernèche; Bernhard Egwolf; Bogdan Lev; Sergei Y Noskov; Christopher N Rowley; Haibo Yu
Journal:  J Gen Physiol       Date:  2011-05       Impact factor: 4.086

View more
  4 in total

1.  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
Journal:  Carbohydr Res       Date:  2018-01-31       Impact factor: 2.104

2.  Molecular Dynamics Simulations of Ionic Liquids and Electrolytes Using Polarizable Force Fields.

Authors:  Dmitry Bedrov; Jean-Philip Piquemal; Oleg Borodin; Alexander D MacKerell; Benoît Roux; Christian Schröder
Journal:  Chem Rev       Date:  2019-05-29       Impact factor: 60.622

Review 3.  An Empirical Polarizable Force Field Based on the Classical Drude Oscillator Model: Development History and Recent Applications.

Authors:  Justin A Lemkul; Jing Huang; Benoît Roux; Alexander D MacKerell
Journal:  Chem Rev       Date:  2016-01-27       Impact factor: 60.622

4.  Bridging Calorimetry and Simulation through Precise Calculations of Cucurbituril-Guest Binding Enthalpies.

Authors:  Andrew T Fenley; Niel M Henriksen; Hari S Muddana; Michael K Gilson
Journal:  J Chem Theory Comput       Date:  2014-07-23       Impact factor: 6.006

  4 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.