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Issue 33, 2018
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Fragment motion in motor molecules: basic concepts and application to intra-molecular rotations

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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.

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

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Article information


Submitted
15 May 2018
Accepted
27 Jul 2018
First published
02 Aug 2018

This article is Open Access

Phys. Chem. Chem. Phys., 2018,20, 21487-21497
Article type
Paper

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

K. E. Hermann, F. Qi, R. Zhao, R. Zhang and M. A. Van Hove, Phys. Chem. Chem. Phys., 2018, 20, 21487
DOI: 10.1039/C8CP03076F

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