Molecular dynamics study of molecular mobility in catenanes

Abstract

Molecular machines described in this paper are meant to be such molecular systems that make use of conformational mobility (i.e. hindered rotation around chemical bonds and molecular construction deformations with formation and breakage of nonvalent bonds). Components of molecular machines move mainly by means of restricted diffusion. As an example of molecular machines of a nonbiological nature catenanes (compounds with two interlocked molecular rings)can be proposed. Thus, for example, model catenane ((2)-(cyclo-bis(paraquat-p-phenylene))-(1(2,6)-tetrathiafulvalena-16(1,5)naphta lena-3, 6, 9, 12, 15, 17, 20, 23, 26, 29-decaoxatnacontaphane)-catenane) changes its redox status when an electric field is applied, and rotation of the rings takes place. It occurs with fixation at certain moments of the influence. To find out characteristic properties of rings movements under various external conditions molecular dynamics simulation was carried out. Three cationic forms of the catenane were first subjected to geometrical optimization and quantum chemical calculation.