Pseudorotation Visualization

If you can read this you need to install java on your computer
This is a visualization of the pseudorotation concept in five-membered rings. You can adjust pseudorotation angle P and the amplitude ν_max by moving the sliders or positioning the cross-hair on the right-hand side graph to see the changes in the conformation. One atom is colored to serve as a reference atom. It can be thought of as the furan oxygen. You can find more information about pseudorotation and conformations of nucleosides and nucleotides in the following papers:
  • J.E. Kilpatrick, K.S. Pitzer, and R. Spitzer, J. Amer. Chem. Soc., 69, 2483 (1947)
  • K.S. Pitzer and W.F. Donath, J. Amer. Chem. Soc., 81, 3213 (1959)
  • C. Altona and M. Sundaralingam, J. Amer. Chem. Soc., 94, 8205, (1972)
Please note that for large amplitudes ν_max the approximations made in constructing this model might no longer be valid and the resulting 3D representation here should be thought of as a general visual aid tool not a specific molecular structure. This is also the reason why the interactive tools limit selection of ν_max values to 40 degrees or less. The data points shown in red are the pseudorotational parameters for β-nucleosides in the Cambridge Structural Database, as evaluated using our PROSIT tool in:
  • Guangyu Sun, Johannes H. Voigt, Igor V. Filippov, Victor E. Marquez, Marc C. Nicklaus, "PROSIT: Pseudo-Rotational Online Service and Interactive Tool, Applied to a Conformational Survey of Nucleosides and Nucleotides", J. Chem. Inf. Comput. Sci. (in press).

Dr. Igor V. Filippov , SAIC-Frederick, 2004

Last Change: 2004-06-14 M. C. Nicklaus