Crystal Structure Prediction as a Tool for Identifying Components of Disordered Structures from Powder Diffraction: A Case Study of Benzamide II

Theoretical crystal structure prediction (CSP) calculations of molecular crystals often generate structures representative of the components associated with disorder, stacking faults, and polytypism. The powder X-ray diffraction (PXRD) pattern of benzamide II contains diffuse scattering consistent with a disordered structure. Previous attempts to elucidate its ordered structure by PXRD and CSP were incomplete because the average structure is actually a complex superposition of multiple polytypes, thus making structure determination particularly challenging. To address this problem, an approach to modeling such complex structures from PXRD data and CSP in combination with molecular dynamics simulations is proposed. Using this approach, the potential building blocks for polytypes possessing a twodimensional stacking fault structure are identified. For benzamide II polytypes, centric H-bonded amide dimers are found to be the preferred H-bonding motif. The stacking faults are also associated with conformational changes of phenyl rings, in agreement with observed diffraction intensities. A characteristic average structure containing the pertinent one-dimensional motifs is derived.

Automated summary

Modeling complex structures from PXRD data and CSP in combination with molecular dynamics simulations can help identify the potential building blocks for polytypes possessing a twodimensional stacking fault structure, where centric H-bonded amide dimers are found to be the preferred H-bonding motif in benzamide II polytypes. The stacking faults are associated with conformational changes of phenyl rings, leading to a characteristic average structure containing the pertinent one-dimensional motifs.