CSDSymmetry: the definitive database of point-group and space-group symmetry relationships in small-molecule crystal structures

Abstract

An algorithm that perceives molecular symmetry has been applied to ca. 200 000 entries from the Cambridge Structural Database (CSD). For each molecule, the perceived point group, together with crystallographic properties such as space group, occupied Wyckoff positions and number of residues in the asymmetric unit, have been placed in a relational database, CSDSymmetry, using Microsoft Access software. Database queries can be constructed easily to find occurrences of any combination of molecular or crystallographic attributes, and thereby to answer questions on relative distributions. Some typical example queries are given. The inclusion of CSD reference codes enables direct visualization of search results using the Cambridge Crystallographic Data Centre's three-dimensional structure visualizer, Mercury.

Why do crystal structures waste molecular inversion symmetry?

“…In the area of molecular and crystallographic symmetry, the most extensive survey has been reported by Pidcock and co-workers, 11 who have developed and applied the derived database CSDSymmetry. 12,13 This distributed resource lists the symmetry properties of most entries in the CSD, including perceived molecular point groups and crystallographic site-symmetry groups. The results derived from CSDSymmetry to date have been principally statistical (for example, the frequencies with which molecules occupy particular sitesymmetry groups or retain particular molecular symmetry elements as part of the space-group symmetry) and they mostly confirm earlier results derived from smaller datasets.…”

Supramolecular Chirality in Crystalline Assemblies of Bile Acids and Their Derivatives; Three-Axial, Tilt, Helical, and Bundle Chirality

“…Figure 14(e) depicts a bundle of both the left-and right-handed helices with the reverse up-down directions, which corresponds to the crystal structure with space group P2 1 /n. These space groups containing the twofold screw axes frequently appear in organic crystals [103]. …”

Prediction of the crystal structures of axitinib, a polymorphic pharmaceutical molecule

“…The global search was performed over the 59 space groups that appear with the highest frequency in CSDSymmetry (Yao et al, 2002). A total of 4,800,000 candidate structures, each involving one molecule in the asymmetric unit, were generated and used as initial guesses for lattice energy minimization subject to space group symmetry constraints.…”