Fragment motion in motor molecules: basic concepts and application to intra-molecular rotations

Abstract

The complex motion of atoms inside large molecules can be analyzed by considering translation, rotation, and flexibility of corresponding molecular fragments and by applying classical mechanics based on Pulay forces on the atoms, as in molecular dynamics. We propose a fragment motion analysis that provides a basic qualitative understanding of the motion of the different molecular components. Further, it can help to describe or design simplified fragment motions, e.g. the rotation of a rotator with respect to its stator counterpart in a rotor molecule, despite the higher actual complexity due to flexibility of rotator and stator or due to a variable rotation axis. The formal aspects of the fragment motion analysis are discussed in detail. Its application is illustrated by the rotational motion inside the BTP-BCO molecule and by rotational transitions between cis- and trans-stilbene isomers.

Surface-Mounted Dipolar Molecular Rotors Driven by External Electric Field, As Revealed by Torque Analyses

“…To examine the mechanical behavior of a dipolar molecule in an external E -field, we utilize our torque approach as a tool to analyze the intramolecular rotation based on snapshots collected from the rotational trajectory. This torque approach has been validated in previous studies, where we successfully studied the rotational behaviors of a light-driven molecular rotor − and interlocking molecular gears on surfaces. − Moreover, torque analysis is widely used in the study of biophysics, such as the transcription of RNA polymerase, , F1-ATPase, bacterial flagellar motor, , and kinesin . In this study, we extend the torque approach to the investigation of E -field-driven molecular motors.…”

How Does the Flexibility of Molecules Affect the Performance of Molecular Rotors?

“…The torque analysis scheme proposed in our previous work (see also further applications ,, ) is adopted here as a convenient way to evaluate the relationship between curvature and applied forces in a rotor molecule: the Pulay forces obtained from a single-point self-consistent field calculation can serve to obtain this relationship. Taking the 5-arm gear shown in Figure as an example, the rotational axis is chosen as the surface normal of the graphene sheet, passing through the manganese atom (the pivot); then the total torque acting on the whole rotor (thus inducing its rotation) is summed as where the index i runs over all the atoms that constitute the rotor (here 10 C atoms and 5 N atoms), F⃗ i is the Pulay force acting on atom i , and r⃗ i is the corresponding vector from the pivot (the Mn atom) to the position of atom i .…”

Multi-functional switch effect in interlocking molecular rotators-on-graphene systems using electric fields

“…The flexibility of different side groups serving as gear arms (without an electric field) for similar gear molecules has been studied recently, indicating that the C 6 (CN) 6 molecule is a good choice as a model gear system for the study of the effects of an applied electric field. 64,65 Using DFT calculations, we can obtain the total energy to evaluate the stability of the system, as shown in Fig. 3a.…”