Paper Citing NAMD - Abstract
Liu, Peng; Shao, Xueguang; Cai, Wensheng
Deciphering the Mechanism Involved in the Switch On/Off of Molecular Pistons
CHINESE JOURNAL OF CHEMISTRY, 33:1199-1205, OCT 2015
Manufacturing machines converting energy to mechanical work at the molecular level is a vital pathway to explore the microscopic world. A kind of operable molecular engines, composed of -cyclodextrin (-CD), aryl, alkene and amide moiety was investigated using molecular dynamics simulations combined with free-energy calculations. To understand how the integrated alkene double bond controls the work performed on the engines, two alkene isomers of the prototype were considered as two molecular engines. The free-energy profiles delineating the binding process of the amide (Z)- and (E)-isomers for each alkene isomer with 1-adamantanol indicate that for the alkene (E)-isomer, the apparent work performed on the amide bond is 1.6 kcal/mol, while the alkene (Z)-isomer is incapable to perform work. Direct switch on/off of engines caused by the isomerization of the alkene bond was, therefore, witnessed, in line with experimental measurements. Decomposition of the free-energy profile into different components and structural analyses suggest that the isomerization of the alkene bond controls the position of the aryl unit relative to the cavity of the CD, resulting in the difference among the free-energy profiles and the stark contrast of the work performed on engines.
