Literature DB >> 23343286

Six-site polarizable model of water based on the classical Drude oscillator.

Wenbo Yu1, Pedro E M Lopes, Benoît Roux, Alexander D MacKerell.   

Abstract

A polarizable water model, SWM6, was developed and optimized for liquid phase simulations under ambient conditions. Building upon the previously developed SWM4-NDP model, additional sites representing oxygen lone-pairs were introduced. The geometry of the sites is assumed to be rigid. Considering the large number of adjustable parameters, simulated annealing together with polynomial fitting was used to facilitate model optimization. The new water model was shown to yield the correct self-diffusion coefficient after taking the system size effect into account, and the dimer geometry is better reproduced than in the SWM4 models. Moreover, the experimental oxygen-oxygen radial distribution is better reproduced, indicating that the new model more accurately describes the local hydrogen bonding structure of bulk phase water. This was further validated by its ability to reproduce the experimental nuclear magnetic shielding and related chemical shift of the water hydrogen in the bulk phase, a property sensitive to the local hydrogen bonding structure. In addition, comparison of the liquid properties of the SWM6 model is made with those of a number of widely used additive and polarizable models. Overall, improved balance between the description of monomer, dimer, clustered, and bulk phase water is obtained with the new model compared to its SWM4-NDP polarizable predecessor, though application of the model requires an approximately twofold increase on computational resources.

Entities:  

Mesh:

Substances:

Year:  2013        PMID: 23343286      PMCID: PMC3562330          DOI: 10.1063/1.4774577

Source DB:  PubMed          Journal:  J Chem Phys        ISSN: 0021-9606            Impact factor:   3.488


  36 in total

1.  A comparison of the value of viscosity for several water models using Poiseuille flow in a nano-channel.

Authors:  A P Markesteijn; Remco Hartkamp; S Luding; J Westerweel
Journal:  J Chem Phys       Date:  2012-04-07       Impact factor: 3.488

2.  A classical polarizable model for simulations of water and ice.

Authors:  Linda Viererblová; Jiří Kolafa
Journal:  Phys Chem Chem Phys       Date:  2011-09-29       Impact factor: 3.676

3.  Structures of cage, prism, and book isomers of water hexamer from broadband rotational spectroscopy.

Authors:  Cristóbal Pérez; Matt T Muckle; Daniel P Zaleski; Nathan A Seifert; Berhane Temelso; George C Shields; Zbigniew Kisiel; Brooks H Pate
Journal:  Science       Date:  2012-05-18       Impact factor: 47.728

4.  NMR chemical shifts as a tool to analyze first principles molecular dynamics simulations in condensed phases: the case of liquid water.

Authors:  Douglas R Banyai; Tatiana Murakhtina; Daniel Sebastiani
Journal:  Magn Reson Chem       Date:  2010-12       Impact factor: 2.447

5.  Dielectric constant of ices and water: a lesson about water interactions.

Authors:  J L Aragones; L G MacDowell; C Vega
Journal:  J Phys Chem A       Date:  2010-09-24       Impact factor: 2.781

6.  Atomic Level Anisotropy in the Electrostatic Modeling of Lone Pairs for a Polarizable Force Field Based on the Classical Drude Oscillator.

Authors:  Edward Harder; Victor M Anisimov; Igor V Vorobyov; Pedro E M Lopes; Sergei Y Noskov; Alexander D MacKerell; Benoît Roux
Journal:  J Chem Theory Comput       Date:  2006-11       Impact factor: 6.006

7.  Development of transferable interaction potentials for water. V. Extension of the flexible, polarizable, Thole-type model potential (TTM3-F, v. 3.0) to describe the vibrational spectra of water clusters and liquid water.

Authors:  George S Fanourgakis; Sotiris S Xantheas
Journal:  J Chem Phys       Date:  2008-02-21       Impact factor: 3.488

8.  A second generation distributed point polarizable water model.

Authors:  Revati Kumar; Fang-Fang Wang; Glen R Jenness; Kenneth D Jordan
Journal:  J Chem Phys       Date:  2010-01-07       Impact factor: 3.488

9.  Attraction of iodide ions by the free water surface, revealed by simulations with a polarizable force field based on Drude oscillators.

Authors:  Georgios Archontis; Epameinondas Leontidis; Georgia Andreou
Journal:  J Phys Chem B       Date:  2005-09-29       Impact factor: 2.991

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
View more
  37 in total

1.  An Estimation of Hybrid Quantum Mechanical Molecular Mechanical Polarization Energies for Small Molecules Using Polarizable Force-Field Approaches.

Authors:  Jing Huang; Ye Mei; Gerhard König; Andrew C Simmonett; Frank C Pickard; Qin Wu; Lee-Ping Wang; Alexander D MacKerell; Bernard R Brooks; Yihan Shao
Journal:  J Chem Theory Comput       Date:  2017-01-24       Impact factor: 6.006

2.  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

3.  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

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

Authors:  Hui Li; Janamejaya Chowdhary; Lei Huang; Xibing He; Alexander D MacKerell; Benoît Roux
Journal:  J Chem Theory Comput       Date:  2017-08-08       Impact factor: 6.006

6.  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

7.  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

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

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

Authors:  Fang-Yu Lin; Jing Huang; Poonam Pandey; Chetan Rupakheti; Jing Li; Benoı T Roux; Alexander D MacKerell
Journal:  J Chem Theory Comput       Date:  2020-04-27       Impact factor: 6.006

10.  United polarizable multipole water model for molecular mechanics simulation.

Authors:  Rui Qi; Lee-Ping Wang; Qiantao Wang; Vijay S Pande; Pengyu Ren
Journal:  J Chem Phys       Date:  2015-07-07       Impact factor: 3.488

View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.