Literature DB >> 22360206

Correlations in liquid water for the TIP3P-Ewald, TIP4P-2005, TIP5P-Ewald, and SWM4-NDP models.

David J Huggins1.   

Abstract

Water is one of the simplest molecules in existence, but also one of the most important in biological and engineered systems. However, understanding the structure and dynamics of liquid water remains a major scientific challenge. Molecular dynamics simulations of liquid water were performed using the water models TIP3P-Ewald, TIP4P-2005, TIP5P-Ewald, and SWM4-NDP to calculate the radial distribution functions (RDFs), the relative angular distributions, and the excess enthalpies, entropies, and free energies. In addition, lower-order approximations to the entropy were considered, identifying the fourth-order approximation as an excellent estimate of the full entropy. The second-order and third-order approximations are ~20% larger and smaller than the true entropy, respectively. All four models perform very well in predicting the radial distribution functions, with the TIP5P-Ewald model providing the best match to the experimental data. The models also perform well in predicting the excess entropy, enthalpy, and free energy of liquid water. The TIP4P-2005 and SWM4-NDP models are more accurate than the TIP3P-Ewald and TIP5P-Ewald models in this respect. However, the relative angular distribution functions of the four water models reveal notable differences. The TIP5P-Ewald model demonstrates an increased preference for water molecules to act both as tetrahedral hydrogen bond donors and acceptors, whereas the SWM4-NDP model demonstrates an increased preference for water molecules to act as planar hydrogen bond acceptors. These differences are not uncovered by analysis of the RDFs or the commonly employed tetrahedral order parameter. However, they are expected to be very important when considering water molecules around solutes and are thus a key consideration in modelling solvent entropy.
© 2012 American Institute of Physics

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Year:  2012        PMID: 22360206      PMCID: PMC4766739          DOI: 10.1063/1.3683447

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


  28 in total

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2.  Towards an assessment of the accuracy of density functional theory for first principles simulations of water.

Authors:  Jeffrey C Grossman; Eric Schwegler; Erik W Draeger; François Gygi; Giulia Galli
Journal:  J Chem Phys       Date:  2004-01-01       Impact factor: 3.488

3.  A reoptimization of the five-site water potential (TIP5P) for use with Ewald sums.

Authors:  Steven W Rick
Journal:  J Chem Phys       Date:  2004-04-01       Impact factor: 3.488

4.  Scalable molecular dynamics with NAMD.

Authors:  James C Phillips; Rosemary Braun; Wei Wang; James Gumbart; Emad Tajkhorshid; Elizabeth Villa; Christophe Chipot; Robert D Skeel; Laxmikant Kalé; Klaus Schulten
Journal:  J Comput Chem       Date:  2005-12       Impact factor: 3.376

5.  Energetics of hydrogen bond network rearrangements in liquid water.

Authors:  Jared D Smith; Christopher D Cappa; Kevin R Wilson; Benjamin M Messer; Ronald C Cohen; Richard J Saykally
Journal:  Science       Date:  2004-10-29       Impact factor: 47.728

6.  Structural properties of water: comparison of the SPC, SPCE, TIP4P, and TIP5P models of water.

Authors:  Jan Zielkiewicz
Journal:  J Chem Phys       Date:  2005-09-08       Impact factor: 3.488

7.  Extraction of configurational entropy from molecular simulations via an expansion approximation.

Authors:  Benjamin J Killian; Joslyn Yundenfreund Kravitz; Michael K Gilson
Journal:  J Chem Phys       Date:  2007-07-14       Impact factor: 3.488

8.  Role of the active-site solvent in the thermodynamics of factor Xa ligand binding.

Authors:  Robert Abel; Tom Young; Ramy Farid; Bruce J Berne; Richard A Friesner
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9.  The inhomogeneous structure of water at ambient conditions.

Authors:  C Huang; K T Wikfeldt; T Tokushima; D Nordlund; Y Harada; U Bergmann; M Niebuhr; T M Weiss; Y Horikawa; M Leetmaa; M P Ljungberg; O Takahashi; A Lenz; L Ojamäe; A P Lyubartsev; S Shin; L G M Pettersson; A Nilsson
Journal:  Proc Natl Acad Sci U S A       Date:  2009-08-13       Impact factor: 11.205

10.  Thermodynamics of buried water clusters at a protein-ligand binding interface.

Authors:  Zheng Li; Themis Lazaridis
Journal:  J Phys Chem B       Date:  2006-01-26       Impact factor: 2.991

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  13 in total

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

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Journal:  Chem Rev       Date:  2019-05-29       Impact factor: 60.622

3.  Interfacial interaction-driven rheological properties of quartz nanofluids from molecular dynamics simulations and density functional theory calculations.

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4.  Estimation of Solvation Entropy and Enthalpy via Analysis of Water Oxygen-Hydrogen Correlations.

Authors:  Camilo Velez-Vega; Daniel J J McKay; Tom Kurtzman; Vibhas Aravamuthan; Robert A Pearlstein; José S Duca
Journal:  J Chem Theory Comput       Date:  2015-10-21       Impact factor: 6.006

5.  Benchmarking the thermodynamic analysis of water molecules around a model beta sheet.

Authors:  David J Huggins
Journal:  J Comput Chem       Date:  2012-03-27       Impact factor: 3.376

6.  Assimilating Radial Distribution Functions To Build Water Models with Improved Structural Properties.

Authors:  Alexander D Wade; Lee-Ping Wang; David J Huggins
Journal:  J Chem Inf Model       Date:  2018-08-30       Impact factor: 4.956

7.  Combining solvent thermodynamic profiles with functionality maps of the Hsp90 binding site to predict the displacement of water molecules.

Authors:  Kamran Haider; David J Huggins
Journal:  J Chem Inf Model       Date:  2013-10-15       Impact factor: 4.956

8.  Comparing distance metrics for rotation using the k-nearest neighbors algorithm for entropy estimation.

Authors:  David J Huggins
Journal:  J Comput Chem       Date:  2013-12-05       Impact factor: 3.376

9.  Assessing the accuracy of inhomogeneous fluid solvation theory in predicting hydration free energies of simple solutes.

Authors:  David J Huggins; Mike C Payne
Journal:  J Phys Chem B       Date:  2013-06-26       Impact factor: 2.991

10.  From molecular dynamics to Brownian dynamics.

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Journal:  Proc Math Phys Eng Sci       Date:  2014-07-08       Impact factor: 2.704

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