Paper Citing NAMD - Abstract
Liu, Ying; Chipot, Christophe; Shao, Xueguang; Cai, Wensheng
What causes tumbling of altro-alpha-CD derivatives? Insight from computer simulations
RSC ADVANCES, 5:57309-57317, 2015
In water, a remarkable motion can be observed with a [2] rotaxane, wherein the rotor translocates by reeling its axle in the cavity of an altro-alpha-CD stopper. Similarly, in aqueous solution, an alkyl altro-alpha-CD dimer reels its alkyl chain in the altro-alpha-CD cavity to form a pseudo[1] rotaxane dimer. This reeling motion is in fact induced by the tumbling of the altropyranose unit of an altro-alpha-CD, a process shown to be solvent-dependent. Tumbling, however, does not occur in low-polarity solvents such as methanol and DMSO. In the present contribution, the mechanism that underlies solvent-controlled tumbling has been studied at the atomic level by means of molecular dynamics simulations combined with microsecond-timescale free-energy calculations. The free-energy profile delineating the tumbling in water of the altropyranose unit of an alkyl altro-alpha-CD indicates that a 19.8 kcal mol(-1) barrier must be overcome to yield the self-inclusion complex, which is the most stable state available to the supramolecular assembly. In DMSO, the free-energy barrier is about 21.0 kcal mol(-1) higher, and the self-included alkyl altro-alpha-CD corresponds to a metastable state. These results provide new thermodynamic and kinetic insights into solvent-controlled tumbling, and reveal the essence of different experimental observations. Further investigation shows that aside from the polarity of the solvent, tumbling of the altro-alpha-CD derivative stems from the hydrophobicity of the side chain and the propensity of the former to include the latter, which opens perspectives for the design of new, related supramolecular assemblies.
