Animations of Resorcinarene Simulations
Hahn, David F.
Rights / licenseCreative Commons Attribution 4.0 International
A key feature of resorcinarene 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 resorcinarene 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
ContributorsContact person: Hahn, David F.
Data collector: Hahn, David F.
Producer: Hahn, David F.
Research group: Hünenberger, Philippe H.
SoftwareThe 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.)
SubjectMolecular Dynamics; Resorcarenes; Free energy; resorcinarene cavitands; Resorcinarene switches
Organisational unit08820 - 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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