Paper Citing NAMD - Abstract
Zhao, Xiongce
Interaction of C-60 derivatives and ssDNA from simulations
JOURNAL OF PHYSICAL CHEMISTRY C, 112:8898-8906, JUN 19 2008
We report atomistic modeling studies on the interaction of water-soluble C-60 derivatives and single-stranded DNA (ssDNA) segments in phosphate-buffered solutions. Stable hybrids are formed by C-60 derivatives and ssDNA segments, with binding energies in the range of -23 to -47 kcal/mol. By contrast, the typical binding energy between two C-60 derivative molecules is -11 to -15 kcal/mol. The binding pattern of C-60 derivatives with ssDNA molecules depends on the size and shape of the C-60 functional groups. For C-60 derivatives with functional groups that contain aromatic rings, strong pi stacking was observed between the ssDNA base rings and the functional benzene rings. For C-60 derivatives with a long hydrophilic chain, the binding is greatly enhanced by the hydrophilic interaction from the entanglement between the chain and the ssDNA backbone. Stable hydrogen bonds were observed between the hydroxyl hydrogen on the functional chain and the phosphate oxygen on the ssDNA backbone. For C-60 derivative with short hydrophilic groups, at least two binding patterns were observed, one of which is dominated by the hydrophobic interaction between the C-60 surface and bases on ssDNA, and the other involves multiple weak hydrogen bonds between the functional carboxylic groups and ssDNA.
