Molecular dynamics study of molecular mobility in catenanes

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)

Molecular dynamics study of molecular mobility in catenanes

Ye.V. Tourleigh1, a, K.V. Shaitan 1, b

1Moscow State University, Faculty of Biology, Dept. of Bioengineering, 119899 Moscow, Russia

ayegr@moldyn.ru, bshaitan@moldyn.ru

Keywords: molecular machines, molecular dynamics, stochasticity, catenanes, restricted diffusion.

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)naphtalena-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.

Introduction

Drawing macroscopic analogies on the phenomena of molecular level establishes relationships between two approaches to studying structure of substance – large-downward (top-down) and small-upward (bottom-up) ones. In this connection, molecular machines present an image which

could be characterized not only by the features

that reside in ordinary systems of molecular

level, but also by the terms that describe large

constructions. Of course, dynamics of a

molecular machine, generally, a set of

components (molecules, groups of atoms), is

stochastic to a great extent [1]. That is caused by

movement of elements of the machine by the

mechanism of restricted diffusion [2].

Nevertheless, at the appropriate influence

components can make movements similar to

mechanical – predominance of large-scale

displacements in a certain direction and

conformational transitions are observed. An

experimentally well investigated example of

molecular machines is catenanes which are

compounds consisting of two interlocked

molecular rings [3].

Fig. 1. (A) Molecular drawing of the bistable Practical application of catenanes has been

[2]catenane. The voltage-driven circumrotation of co-already investigated in light of their possible use conformer [A0] to co-conformer [B+] is the basis of as semi-conductor switches in logic circuits of the device. (B) Proposed mechanochemical elementary computers [4]. In the proposed mechanism for the operation of the molecular switch. model the catenane, being between two (Reproduced from [4] with courteous permission of electrodes, changes its oxidation status under the the authors).