Paper Citing NAMD - Abstract
Wang Shuangshuang; Liu Peng; Cai Wensheng; Shao Xueguang
Effect of Hydrophobicity of Threads on the Solvent-controlled Shuttling in Rotaxanes
CHEMICAL JOURNAL OF CHINESE UNIVERSITIES-CHINESE, 36:2211-2219, NOV 10 2015
In order to investigate the hydrophobic effect of chain-like structures on shuttling in further, three similar rotaxanes are studied in this work. The rotaxanes are formed by an alpha-CD, two dodecamethylene chains (ALK) or two poly (ethylene glycol) (PEG) for stations, one bipyridinium moiety (PY) or one biphenyl moiety(PH) for linkers and large end groups at both sides. The shuttling of the rotaxanes was studied by means of molecular dynamics simulations(MD) combined with free-energy calculations in water and DMSO at room temperature. Two methods, the adaptive biasing force (ABF) method and the multiple walker ABF (MW-ABF) method, a modified version of ABF, are adopted for calculating the free-energy change characterizing the shuttling process. The potentials of mean force(PMFs) for the three rotaxanes are determined. The free-energy barriers of the PMFs for the PEG-rotaxane are lower than those for the the ALK-rotaxane both in water and DMSO. Furthermore, the barriers for the PEG-rotaxanes in DMSO are lower than that in water, which is in accordance with the ALK-rotaxanes. The barriers for the PH-rotaxanes are significantly lower than those for the PY-rotaxanes. Partitioning the PMFs into free-energy components suggests that change of the the charged group by an hydrophobic biphenyl moiety or decrease of the hydrophobicity of the chain-like structure in two stations from ALK to PEG reduces the free-energy barrier with respect to the stable states in the stations. In addition, comparison of the two free-energy calculation methods shows that the MW-ABF method can significantly improve the uniformity of sampling and hence increase the computational efficiency.
