Literature DB >> 20831149

Comparing simulated and experimental translation and rotation constants: range of validity for viscosity scaling.

Richard M Venable1, Elizabeth Hatcher, Olgun Guvench, Alexander D Mackerell, Richard W Pastor.   

Abstract

Proper simulation of dynamic properties, including molecular diffusion, is an important goal of empirical force fields. However, the widely used TIP3P water model does not reproduce the experimental viscosity of water. Consequently, scaling of simulated diffusion constants of solutes in aqueous solutions is required to effectively compare them with experiment. It is proposed that scaling by the ratio of viscosities of model and real water is appropriate in the regime where the concentration dependence of simulated and experimental solution viscosities is parallel. With this ansatz, viscosity scaling can be carried out for glucose and trehalose up to 20 wt % for simulations carried out with the CHARMM additive carbohydrate force field C35 and TIP3P water; above this value, the concentration dependence of simulated viscosities lags that of experiment, and scaling is not advised. Scaled translational diffusion constants for glucose and the disaccharides trehalose, maltose, and melibiose at low concentration agree nearly quantitatively with experiment, as do NMR (13)C T(1)'s for glucose, trehalose, and maltose; these results support the use of C35 for simulations of sugar transport properties at low concentration. At high concentrations the scaled diffusion constants for glucose and trehalose underestimate and overestimate experiment, respectively. Hydrodynamic bead model calculations indicate a hydration level of approximately 1 water/hydroxyl for glucose. Patterns for the disaccharides are more complicated, though trehalose binds 0.5 to 1 more water than does maltose depending on the analysis.

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Year:  2010        PMID: 20831149      PMCID: PMC3040444          DOI: 10.1021/jp105549s

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


  14 in total

1.  c,T-dependence of the viscosity and the self-diffusion coefficients in some aqueous carbohydrate solutions.

Authors:  M Rampp; C Buttersack; H D Lüdemann
Journal:  Carbohydr Res       Date:  2000-10-06       Impact factor: 2.104

2.  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

Review 3.  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

4.  Using the isotropic periodic sum method to calculate long-range interactions of heterogeneous systems.

Authors:  Xiongwu Wu; Bernard R Brooks
Journal:  J Chem Phys       Date:  2008-10-21       Impact factor: 3.488

5.  Canonical dynamics: Equilibrium phase-space distributions.

Authors: 
Journal:  Phys Rev A Gen Phys       Date:  1985-03

Review 6.  Hydrodynamic properties of complex, rigid, biological macromolecules: theory and applications.

Authors:  J G Garcia de la Torre; V A Bloomfield
Journal:  Q Rev Biophys       Date:  1981-02       Impact factor: 5.318

7.  Molecular dynamics studies of polyethylene oxide and polyethylene glycol: hydrodynamic radius and shape anisotropy.

Authors:  Hwankyu Lee; Richard M Venable; Alexander D Mackerell; Richard W Pastor
Journal:  Biophys J       Date:  2008-05-02       Impact factor: 4.033

8.  Comparison of the extended isotropic periodic sum and particle mesh Ewald methods for simulations of lipid bilayers and monolayers.

Authors:  Richard M Venable; Linda E Chen; Richard W Pastor
Journal:  J Phys Chem B       Date:  2009-04-30       Impact factor: 2.991

9.  Application of NMR, molecular simulation, and hydrodynamics to conformational analysis of trisaccharides.

Authors:  Ann M Dixon; Richard Venable; Göran Widmalm; T E Bull; Richard W Pastor
Journal:  Biopolymers       Date:  2003-08       Impact factor: 2.505

10.  Additive empirical force field for hexopyranose monosaccharides.

Authors:  Olgun Guvench; Shannon N Greene; Ganesh Kamath; John W Brady; Richard M Venable; Richard W Pastor; Alexander D Mackerell
Journal:  J Comput Chem       Date:  2008-11-30       Impact factor: 3.376

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  16 in total

Review 1.  Recent advances in macromolecular hydrodynamic modeling.

Authors:  Sergio R Aragon
Journal:  Methods       Date:  2010-11-10       Impact factor: 3.608

2.  Brownian dynamics simulations of ion transport through the VDAC.

Authors:  Kyu Il Lee; Huan Rui; Richard W Pastor; Wonpil Im
Journal:  Biophys J       Date:  2011-02-02       Impact factor: 4.033

Review 3.  Molecular Dynamics Simulations of Membrane Permeability.

Authors:  Richard M Venable; Andreas Krämer; Richard W Pastor
Journal:  Chem Rev       Date:  2019-02-12       Impact factor: 60.622

4.  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

5.  Understanding how water models affect the anomalous pressure dependence of their diffusion coefficients.

Authors:  Xiaojing Teng; Bailang Liu; Toshiko Ichiye
Journal:  J Chem Phys       Date:  2020-09-14       Impact factor: 3.488

6.  Surface Shear Viscosity and Interleaflet Friction from Nonequilibrium Simulations of Lipid Bilayers.

Authors:  Andrew Zgorski; Richard W Pastor; Edward Lyman
Journal:  J Chem Theory Comput       Date:  2019-09-30       Impact factor: 6.006

7.  HullRad: Fast Calculations of Folded and Disordered Protein and Nucleic Acid Hydrodynamic Properties.

Authors:  Patrick J Fleming; Karen G Fleming
Journal:  Biophys J       Date:  2018-02-27       Impact factor: 4.033

8.  Position-Dependent Diffusion Tensors in Anisotropic Media from Simulation: Oxygen Transport in and through Membranes.

Authors:  An Ghysels; Richard M Venable; Richard W Pastor; Gerhard Hummer
Journal:  J Chem Theory Comput       Date:  2017-05-19       Impact factor: 6.006

9.  Development of the CHARMM Force Field for Lipids.

Authors:  R W Pastor; A D Mackerell
Journal:  J Phys Chem Lett       Date:  2011       Impact factor: 6.475

Review 10.  Mechanical properties of lipid bilayers from molecular dynamics simulation.

Authors:  Richard M Venable; Frank L H Brown; Richard W Pastor
Journal:  Chem Phys Lipids       Date:  2015-07-31       Impact factor: 3.329

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