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Updated: Jun 20, 2026
Modeling Ligands into Maps Derived from Electron Cryomicroscopy
Published on: July 19, 2024
Structure and conformational analysis of a bidentate pro-ligand, C21H34N2S2, from powder synchrotron diffraction data
Edward E Avila1, Asiloé J Mora, Gerzon E Delgado
1Laboratorio de Cristalografía, Departamento de Química, Facultad de Ciencias, Universidad de Los Andes 5101, Venezuela.
Abstract:
The molecular and crystalline structure of ethyl 1',2',3',4',4a',5',6',7'-octahydrodispiro[cyclohexane-1,2'-quinazoline-4',1''-cyclohexane]-8'-carbodithioate (I) was solved and refined from powder synchrotron X-ray diffraction data. The initial model for the structural solution in direct space using the simulated annealing algorithm implemented in DASH [David et al. (2006). J. Appl. Cryst. 39, 910-915] was obtained performing a conformational study on the fused six-membered rings of the octahydroquinazoline system and the two spiran cyclohexane rings of (I). The best model was chosen using experimental evidence from 1H and 13C NMR [Contreras et al. (2001). J. Heterocycl. Chem. 38, 1223-1225] in combination with semi-empirical AM1 calculations. In the refined structure the two spiran rings have the chair conformation, while both of the fused rings in the octahydroquinazoline system have half-chair conformations compared with in-vacuum density-functional theory (DFT) B3LYP/6-311G*, DFTB (density-functional tight-binding) theoretical calculations in the solid state and other related structures from X-ray diffraction data. Compound (I) presents weak intramolecular hydrogen bonds of the type N-H...S and C-H...S, which produce delocalization of the electron density in the generated rings described by graph symbols S(6) and S(5). Packing of the molecules is dominated by van der Waals interactions.
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