Literature DB >> 17425357

Long-range Lennard-Jones and electrostatic interactions in interfaces: application of the isotropic periodic sum method.

Jeffery B Klauda1, Xiongwu Wu, Richard W Pastor, Bernard R Brooks.   

Abstract

Molecular dynamics (MD) simulations of heptane/vapor, hexadecane/vapor, water/vapor, hexadecane/water, and dipalmitoylphosphatidylcholine (DPPC) bilayers and monolayers are analyzed to determine the accuracy of treating long-range interactions in interfaces with the isotropic periodic sum (IPS) method. The method and cutoff (rc) dependences of surface tensions, density profiles, water dipole orientation, and electrostatic potential profiles are used as metrics. The water/vapor, heptane/vapor, and hexadecane/vapor interfaces are accurately and efficiently calculated with 2D IPS (rc=10 A). It is demonstrated that 3D IPS is not practical for any of the interfacial systems studied. However, the hybrid method PME/IPS [Particle Mesh Ewald for electrostatics and 3D IPS for Lennard-Jones (LJ) interactions] provides an efficient way to include both types of long-range forces in simulations of large liquid/vacuum and all liquid/liquid interfaces, including lipid monolayers and bilayers. A previously published pressure-based long-range LJ correction yields results similar to those of PME/IPS for liquid/liquid interfaces. The contributions to surface tension of LJ terms arising from interactions beyond 10 A range from 13 dyn/cm for the hexadecane/vapor interface to approximately 3 dyn/cm for hexadecane/water and DPPC bilayers and monolayers. Surface tensions of alkane/vapor, hexadecane/water, and DPPC monolayers based on the CHARMM lipid force fields agree very well with experiment, whereas surface tensions of the TIP3P and TIP4P-Ew water models underestimate experiment by 16 and 11 dyn/cm, respectively. Dipole potential drops (DeltaPsi) are less sensitive to long-range LJ interactions than surface tensions. However, DeltaPsi for the DPPC bilayer (845+/-3 mV proceeding from water to lipid) and water (547+/-2 mV for TIP4P-Ew and 521+/-3 mV for TIP3P) overestimate experiment by factors of 3 and 5, respectively, and represent expected deficiencies in nonpolarizable force fields.

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Year:  2007        PMID: 17425357      PMCID: PMC6413507          DOI: 10.1021/jp068767m

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


  24 in total

Review 1.  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

2.  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

3.  Surface Penetration without Enrichment: Simulations Show Ion Surface Propensities Consistent with Both Elevated Surface Tension and Surface Sensitive Spectroscopy.

Authors:  Jicun Li; Feng Wang
Journal:  J Phys Chem B       Date:  2019-08-13       Impact factor: 2.991

4.  Isotropic periodic sum of electrostatic interactions for polar systems.

Authors:  Xiongwu Wu; Bernard R Brooks
Journal:  J Chem Phys       Date:  2009-07-14       Impact factor: 3.488

5.  Origin of pKa Shifts of Internal Lysine Residues in SNase Studied Via Equal-Molar VMMS Simulations in Explicit Water.

Authors:  Xiongwu Wu; Juyong Lee; Bernard R Brooks
Journal:  J Phys Chem B       Date:  2016-10-18       Impact factor: 2.991

6.  Exploring the free-energy landscapes of biological systems with steered molecular dynamics.

Authors:  L Y Chen
Journal:  Phys Chem Chem Phys       Date:  2011-02-25       Impact factor: 3.676

7.  Application of Molecular Dynamics Simulations in Molecular Property Prediction I: Density and Heat of Vaporization.

Authors:  Junmei Wang; Hou Tingjun
Journal:  J Chem Theory Comput       Date:  2011-07-12       Impact factor: 6.006

8.  Force Fields for Small Molecules.

Authors:  Fang-Yu Lin; Alexander D MacKerell
Journal:  Methods Mol Biol       Date:  2019

9.  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

10.  Effects of truncating van der Waals interactions in lipid bilayer simulations.

Authors:  Kun Huang; Angel E García
Journal:  J Chem Phys       Date:  2014-09-14       Impact factor: 3.488

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