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. 2010 Feb 5;486(1-3):70-73.
doi: 10.1016/j.cplett.2009.12.089.

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

Jerez A Te  1 , Ming-Liang Tan, Toshiko Ichiye
Affiliations

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

Jerez A Te et al. Chem Phys Lett. .

Abstract

The soft sticky dipole-quadrupole-octupole (SSDQO) potential energy function represents a water molecule by a single site with a van der Waals sphere and point multipoles. Previously, SSDQO was shown to give good properties for liquid water and solvation of simple ions and is faster than three point models. Here, SSDQO is assessed for solvating biologically relevant molecules having a multi-site, partial charge description. Monte Carlo simulations of ethanol, benzene, and N-methylacetamide in SSDQO with SPC/E moments showed the water structure was as good as in SPC/E. Thus, SSDQO is potentially useful for simulations of biological macromolecules in aqueous solution.

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Figures

Figure 1
Figure 1
Radial distribution for liquid water: oxygen – oxygen, oxygen – hydrogen (shifted upward by 1), and hydrogen – hydrogen (shifted upward by 2) for SSDQO (black) and SPC/E (gray) water.
Figure 2
Figure 2
Radial distribution functions for ethanol in SSDQO (black) and SPC/E (gray) water: a) ethanol oxygen - water oxygen, ethanol oxygen - water hydrogen (shifted upward by 1), and ethanol hydrogen – water oxygen (shifted upwards by 2) and b) ethanol methyl carbon – water oxygen and ethanol methyl carbon – water hydrogen (shifted by 2).
Figure 3
Figure 3
Radial distribution functions for benzene in SSDQO (black) and SPC/E (gray) water: a) benzene carbon - water oxygen and benzene carbon - hydrogen (shifted upward by 2) and b) benzene center of mass - water oxygen and benzene center of mass - hydrogen (shifted upward by 2).
Figure 4
Figure 4
Radial distribution functions for N-methylacetamide in SSDQO (black) and SPC/E (gray) water: a) NMA oxygen - water oxygen and NMA oxygen - hydrogen (shifted upward by 2) and b) NMA nitrogen - water oxygen, NMA nitrogen - hydrogen (shifted upward by 1), and NMA hydrogen - oxygen (shifted upward by 2).
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