Animations of Resorcin[4]arene Simulations
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Date
2019-11-11Type
- Video
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Abstract
A key feature of resorcin[4]arene cavitands is their ability to switch between a close/contracted (Vase) and an open/expanded (Kite) conformation. In the present movies, the Vase-Kite transitions of a quinoxaline- and a dinitrobenzene-based resorcin[4]arene are visualized from simulations using explicit-solvent molecular dynamics (MD) in three solvent environments (vacuum, chloroform and toluene) and at three temperatures (198.15, 243.15 and 298.15 K).
A first set of five movies from unbiased MD simulations show a complete Vase-to-Kite transition. as well as between degenerate Kite 1 and Kite 2 forms. Another five movies show solvent-exchange events. A last set of five movies visualize ball-and-stick local elevation umbrella sampling (B&S-LEUS) simulations, which promote interconversion transitions. Show more
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https://doi.org/10.3929/ethz-b-000376729Contributors
Contact person: Hahn, David F.
Data collector: Hahn, David F.
Producer: Hahn, David F.
Research group: Hünenberger, Philippe H.
Publisher
ETH ZurichSoftware
The simulations were performed using a modified version of the GROMOS11 program. (W.F. van Gunsteren, The GROMOS software for biomolecular simulation. Available at: http://www.gromos.net 05/05/2011.; N. Schmid, C.D. Christ, M. Christen, A.P. Eichenberger, W.F. van Gunsteren, Comput. Phys. Commun. 2012, 183, 890: Architecture, implementation and parallelisation of the GROMOS software for biomolecular simulation.; A.-P. E. Kunz, J.R. Allison, D.P. Geerke, B.A.C. Horta, P.H. Hünenberger, S. Riniker, N. Schmid, W.F. van Gunsteren, J. Comput. Chem. 2012, 33, 340: New functionalities in the GROMOS biomolecular
simulation software.)
The movies have been realized with the program Visual Molecular Dynamics (VMD), version 1.9.2. (W. Humphrey, A. Dalke, K. Schulten, J. Mol. Graph. 1996, 14, 33: VMD - Visual molecular dynamics.)Subject
Molecular Dynamics; Resorc[4]arenes; Free energy; resorcin[4]arene cavitands; Resorcin[4]arene switchesOrganisational unit
08820 - Hünenberger, Philippe (Tit.-Prof.)
Related publications and datasets
Is supplement to: http://hdl.handle.net/20.500.11850/344036
Is supplement to: https://doi.org/10.3929/ethz-b-000377256
Is part of: http://hdl.handle.net/20.500.11850/344036
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