CALPUCK: An Open Python Tool for Cremer–Pople Ring Puckering Analysis Including a New 2D Mapping of Seven-Membered Rings

Abstract

Ring puckering is a central conformational phenomenon that strongly influences the structure and reactivity of cyclic and heterocyclic molecules, with particular relevance to carbohydrate chemistry and stereoelectronic effects. Ring puckering represents a critical conformational phenomenon in organic chemistry, where cyclic molecules deviate from planarity through out-of-plane bending motions to minimize steric and electronic strain. To make quantitative puckering analysis more accessible, this work presents a free, open-source Python tool that computes Cremer–Pople puckering parameters for five-, six- and seven-membered rings from standard .xyz coordinates and produces intuitive two-dimensional visualizations of amplitude and phase. The implementation centers on vectorized projections onto sinusoidal basis functions, special-case handling for different ring sizes, and interactive selection of ring atoms; it emphasizes clarity, speed, and explicit support for seven-membered systems often neglected due to the difficulty to represent toroidal landscape. Validation and discussion illustrate how the tool maps canonical envelope, twist, chair, boat, and higher-dimensional pseudorotation landscapes onto readable plots, enabling rapid classification of conformers and interpretation of dynamical motifs. The program provides a practical and accessible implementation for the analysis and visualization of ring conformations based on puckering coordinates.