Quinuclidine thiosemicarbazone crystal structure determination: Quantum insights via Hirshfeld atom refinement and intermolecular interaction energies

Crystal structure of quinuclidine thiosemicarbazone was determined using single crystal Xray diffraction. During crystal structure refinement stage, conventional independent atom model (IAM) was used, as well as quantum crystallographic approach through Hirshfeld atom refinement (HAR). Two HAR approaches were tested, differing in the treatment of crystal filed simulation. In the first strategy, wavefunction was obtained for the central molecule and four additional molecules involved in hydrogen bonding. In the second strategy, wavefunction was obtained for the central molecule which was placed in simulated crystal field of point and dipole charges located at positions of the surrounding molecules’ atoms. In spite of the fact that HAR was performed with suboptimal diffraction data, which was collected in a routine fashion (standard resolution of dmin = 0.8 Å and room temperature), a significant improvement in the resulting geometry and refinement statistics was obtained when compared to the IAM model. HAR resulted in lower R values (2.04%; 2.06%), compared to R=2.94% obtained with IAM refinement. Additionally, during HAR the positions and displacement parameters of all H atoms were successfully refined freely. The mean values for N–H (0.999 Å; 0.993 Å) and C–H (1.081 Å; 1.080 Å) bond lengths are close to (within ±0.01 Å) standard values obtained with neutron diffraction (N–H=1.015 Å; C–H=1.089 Å). Results obtained indicate that HAR could yield significantly improved structural parameters of crystal structures even from routine data collection practices, which advocates its general use in small molecule crystallography. Intermolecular interaction energies were calculated with CrystalExplorer and PIXEL. Data obtained with both methods are in good agreement. The hydrogen bonded dimer with the highest interaction energy (−47 kJ mol−1) is predominantly influenced by electrostatic energy contributions. The second strongest interaction (−43 kJ/mol), also mediated through a hydrogen bond, exhibits an approximately equal contribution from dispersion and electrostatic energies. Additionally, several dispersion interactions with an average energy of −15 kJ mol−1 are observed. In summary, the molecular packing in the crystal is of the framework type, from the energetic perspective.