Small-Molecule Structure Determination and Anisotropic Displacement Analysis at Turkish Light Source

Abstract

Single-crystal X-ray diffraction remains one of the most direct and reliable techniques for clarifying the three-dimensional structures of small molecules; however, its wider use in developing research settings has historically been limited by access to advanced instrumentation. Here, we consider the performance of the in-house diffractometer, Turkish Light Source, for small-molecule structure determination using three rhodanine-derivative compounds. Diffraction data were collected, processed, and followed by full-matrix least-squares refinement as a user-friendly pipeline. The compounds were successfully resolved in the triclinic space group P-1 and refined to chemically reasonable models, although notable differences in data quality and refinement parameters were observed. Compounds 1 and 2 produced the most robust and internally coherent structure, whereas compound 3 displayed refinement tribulations. These might be attributed to the intrinsic structural disorder of c-5b, analogous to polymorphic perversity in higher Z' phase, likely due to the presence of dissymmetric molecules within the asymmetric unit (Z' = 2), rather than empirical limitations. Anisotropic displacement parameters were systematically computed by atom-resolved Ueq factors and anisotropy index. The combined analyses reveal that structural ambiguity of c-5b is largely governed by localized maxima in atomic displacement (up to 0.29 [A]2 in Ueq with 6.67 anisotropy) rather than by global disorder, caused by the fluorinated aryl moiety of c-5b. These findings indicate that the in-house SCXRD system, when coupled with our user-friendly downstream pipeline, can yield reliable structural data for small molecules. Brief video tutorials and detailed SOPs have been provided in the Tutorials folder, including CrysAlisPro and Olex2 tutorials, as well as are easily accessible for users.