Recently we studied the hydration shell formation of uracil and thymine in complexes comprising 11 water molecules using electronic structure methods (DFT and MP2) (1). We have now extended our study to include the cytosine and adenine DNA bases. As found previously, structures showing a clustering of the water molecules were found to be energetically preferred over structures with water distributed around the base and forming a chain (Table I). For cytosine-(H₂O)₁₄, the larger stability of the clustered structure is due to its larger water-water interaction, in agreement with our previous results. For adenine-(H₂O)₁₆ on the other hand, the water-water interaction is of nearly identical magnitude in the two different complexes; the larger stability of the clustered structure appears to be due to an increased base-water interaction. The results indicate that the hydration shell structure is determined by a delicate balance of water-water and base-water interactions.


Figure 1: The MMMT (A and C) and MSM (B and D) derived structures of the cytosine-(H₂O)₁₄ and adenine-(H₂O)₁₆ complexes optimized at the B3LYP/6-31+G(d) level of theory.


References and Footnotes

1. Danilov, V. I., van Mourik, T., Poltev, V. I. Chem Phys Lett 429, 255 (2006).
2. Shishkin, O. V., Gorb, L., Leszczynski, J. J Phys Chem B 104, 5357 (2000).; Sukhanov, O. S., Shishkin, O. V., Gorb, I., Podolyan, Y., Leszczynski, J. J Phys Chem B 107, 2846 (2003).