[MDAKit / Hackathon] Ring Puckering

[IAlibay]

Overview

Ring groups can adopt a variety of “puckered” geometries that influence
their physical and chemical properties. Several formulations exist for
quantifying this puckering, e.g. Pickett angles [Strauss 1970],
Cremer-Pople [Cremer 1975], and Hill-Reilly [Hill 2007].

MDAnalysis currently features tools for assessing puckering in 5-membered
rings in our nucleic acid analysis module;
however, such capabilities are lacking for 6 (or higher) membered rings.

References

1. Strauss, H.L.; Pickett, H.M; Conformational structure, energy and inversion rates of cyclohexane and some related oxanes. J. Am. Chem. Soc. 1970, 92: 7281-7290 https://doi.org/10.1021/ja00728a009
2. Cremer D., Pople, J.A.; General definition of ring puckering coordinates. J. Am. Chem. Soc 1975, 97: 1354-1358 https://doi.org/10.1021/ja00839a011
3. Hill, A. D.; Reilly, P. J. Puckering Coordinates of Monocyclic Rings by Triangular Decomposition. J. Chem. Inf. Model. 2007, 47: 1031– 1035 https://doi.org/10.1021/ci600492e