Literature DB >> 17042615

Dynamical properties of the soft sticky dipole-quadrupole-octupole water model: a molecular dynamics study.

Snehasis Chowdhuri1, Ming-Liang Tan, Toshiko Ichiye.   

Abstract

The dynamical properties of the soft sticky dipole-quadrupole-octupole (SSDQO) water model using SPC/E moments are calculated utilizing molecular dynamics simulations. This new potential for liquid water describes the water-water interactions by a Lennard-Jones term and a sticky potential, which is an approximate moment expansion with point dipole, quadrupole, and octupole moments, and reproduces radial distribution functions of pure liquid water using the moments of SPC/E [Ichiye and Tan, J. Chem. Phys. 124, 134504 (2006)]. The forces and torques of SSDQO water for the dipole-quadrupole, quadrupole-quadrupole, and dipole-octupole interactions are derived here. The simulations are carried out at 298 K in the microcanonical ensemble employing the Ewald method for the long-range dipole-dipole interactions. Here, various dynamical properties associated with translational and rotational motions of SSDQO water using the moments of SPC/E (SSDQO:SPC/E) water are compared with the results from SPC/E and also experiment. The self-diffusion coefficient of SSDQO:SPC/E water is found to be in excellent agreement with both SPC/E and experiment whereas the single particle orientational relaxation time for dipole vector is better than SPC/E water but it is somewhat smaller than experiment. The dielectric constant of SSDQO:SPC/E is essentially identical to SPC/E, and both are slightly lower than experiment. Also, molecular dynamics simulations of the SSDQO water model are found to be about twice as fast as three-site models such as SPC/E.

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Year:  2006        PMID: 17042615     DOI: 10.1063/1.2357117

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


  16 in total

1.  Solvation of Glucose, Trehalose, and Sucrose by the Soft Sticky Dipole-Quadrupole-Octupole Water Model.

Authors:  Jerez A Te; Ming-Liang Tan; Toshiko Ichiye
Journal:  Chem Phys Lett       Date:  2010-05-17       Impact factor: 2.328

2.  UNDERSTANDING STRUCTURAL EFFECTS OF MULTIPOLE MOMENTS ON AQUEOUS SOLVATION OF IONS USING THE SOFT-STICKY DIPOLE-QUADRUPOLE-OCTUPOLE WATER MODEL.

Authors:  Jerez A Te; Toshiko Ichiye
Journal:  Chem Phys Lett       Date:  2010-10-29       Impact factor: 2.328

3.  Solvation of Biomolecules by the Soft Sticky Dipole-Quadrupole-Octupole Water Model.

Authors:  Jerez A Te; Ming-Liang Tan; Toshiko Ichiye
Journal:  Chem Phys Lett       Date:  2010-02-05       Impact factor: 2.328

4.  Temperature and pressure dependence of the optimized soft-sticky dipole-quadrupole-octupole water model.

Authors:  Jerez A Te; Toshiko Ichiye
Journal:  J Chem Phys       Date:  2010-03-21       Impact factor: 3.488

5.  Molecular modeling and dynamics studies of cytidylate kinase from Mycobacterium tuberculosis H37Rv.

Authors:  Rafael Andrade Caceres; Luís Fernando Saraiva Macedo Timmers; Ana Luiza Vivan; Cristopher Zandoná Schneider; Luiz Augusto Basso; Walter Filgueira De Azevedo; Diogenes Santiago Santos
Journal:  J Mol Model       Date:  2008-03-15       Impact factor: 1.810

6.  Incorporating dipolar solvents with variable density in Poisson-Boltzmann electrostatics.

Authors:  Cyril Azuara; Henri Orland; Michael Bon; Patrice Koehl; Marc Delarue
Journal:  Biophys J       Date:  2008-09-26       Impact factor: 4.033

7.  Coarse-graining the electrostatic potential via distributed multipole expansions.

Authors:  Apostol Gramada; Philip E Bourne
Journal:  Comput Phys Commun       Date:  2011-07-01       Impact factor: 4.390

8.  Exploring the molecular basis for selective binding of Mycobacterium tuberculosis Asp kinase toward its natural substrates and feedback inhibitors: a docking and molecular dynamics study.

Authors:  M Chaitanya; B Babajan; C M Anuradha; M Naveen; C Rajasekhar; P Madhusudana; Chitta Suresh Kumar
Journal:  J Mol Model       Date:  2010-02-07       Impact factor: 1.810

9.  Molecular dynamics studies of a hexameric purine nucleoside phosphorylase.

Authors:  Fernando Berton Zanchi; Rafael Andrade Caceres; Rodrigo Guerino Stabeli; Walter Filgueira de Azevedo
Journal:  J Mol Model       Date:  2009-08-11       Impact factor: 1.810

10.  Molecular modeling and dynamics studies of purine nucleoside phosphorylase from Bacteroides fragilis.

Authors:  Ivani Pauli; Luis Fernando Saraiva Macedo Timmers; Rafael Andrade Caceres; Luiz Augusto Basso; Diógenes Santiago Santos; Walter Filgueira de Azevedo
Journal:  J Mol Model       Date:  2009-01-27       Impact factor: 1.810

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