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

Literature Information

Publication Date 2018-08-02
DOI 10.1039/C8CP03076F
Impact Factor 3.676
Authors

Klaus E. Hermann, Fei Qi, Rundong Zhao, Michel A. Van Hove


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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.

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Physical Chemistry Chemical Physics

Physical Chemistry Chemical Physics
CiteScore: 5.5
Self-citation Rate: 10.3%
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Physical Chemistry Chemical Physics (PCCP) is an international journal co-owned by 19 physical chemistry and physics societies from around the world. This journal publishes original, cutting-edge research in physical chemistry, chemical physics and biophysical chemistry. To be suitable for publication in PCCP, articles must include significant innovation and/or insight into physical chemistry; this is the most important criterion that reviewers and Editors will judge against when evaluating submissions. The journal has a broad scope and welcomes contributions spanning experiment, theory, computation and data science. Topical coverage includes spectroscopy, dynamics, kinetics, statistical mechanics, thermodynamics, electrochemistry, catalysis, surface science, quantum mechanics, quantum computing and machine learning. Interdisciplinary research areas such as polymers and soft matter, materials, nanoscience, energy, surfaces/interfaces, and biophysical chemistry are welcomed if they demonstrate significant innovation and/or insight into physical chemistry. Joined experimental/theoretical studies are particularly appreciated when complementary and based on up-to-date approaches.

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