Paper Citing NAMD - Abstract
Du, Hongbo; Wickramasinghe, Sumith Ranil; Qian, Xianghong
Specificity in Cationic Interaction with Poly(N-isopropylacrylamide)
JOURNAL OF PHYSICAL CHEMISTRY B, 117:5090-5101, MAY 2 2013
Classical molecular dynamics (MD) simulations were conducted for PNIPAM in 1 M monovalent alkali chloride salt solutions as well as in 0.5 M divalent Mg2+ and Ca2+ chloride salt solutions. It was found that the strength for the direct alkali ion-amide O binding is Strongly Correlated with the size of the ionic radius. The smallest Lit ion binds strongest to amide O, and the largest Cs+ ion has the weakest interaction with the amide bond. For the divalent Mg2+,and Ca2+ ions, their interactions with the amide bond are weak and appear to be mediated by the water molecules, particularly in the case of Mg2+, resulting from their strong hydration. The direct binding between the cations and amide O requires partial desovlation of the ions: that is energetically unfavorable for Mg2+ and also to a great extent for Ca2+. The higher cation charge makes the electrostatic interaction more favorable but the dehydration process less favorable. This competition between electrostatic interaction and the dehydration :process largely dictates whether the direct binding between the cation and amide O is energetically preferred or not For monovalent alkali ions, it is energetically preferred to bind directly with the amide O. Moreover, Li+ ion is also found to associate strongly with the hydrophobic residues, on PNIPAM.
