Source: http://www.jbsdonline.com/a-pm6-study-hydration-shell-of-nucleic-acid-bases-small-water-clusters-p15619.html
Timestamp: 2019-04-19 18:46:38+00:00

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The hydration shell formation of uracil, thymine, cytosine, and adenine in small water clusters was studied using density functional theory (DFT) (1) and the new semiempirical PM6 method (2). The lowest energy structures from Molecular Mechanics (MM) calculations and structures obtained via the modified scheme of monosolvation [MSM (3)] were used as starting configurations for the geometry optimizations. The MM-derived structures, Figure 1, show a clustering of the water molecules, whereas in the MSM-derived structures the water molecules are distributed around the base in a chain-like formation. In good agreement with our previous DFT results, PM6 calculations predict the clustered structures to be energetically preferred, even though the water-base interaction is larger, Table I, in all complexes except A-(H2O)16. This indicates that methods that overemphasize the base-water interaction, like the MSM scheme, cannot predict the preferred clustering of water molecules around nucleic acid bases.
Figure 1: PM6-optimized structures of the different complexes studied. As starting structure the most favorable structure from MM calculations was employed.
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