Revealing Non-covalent Interactions in Molecular Crystals through Their Experimental Electron Densities

• Published in: Chemistry : a European journal Vol. 18; no. 48; pp. 15523 - 15536
• Main Authors: Saleh, Gabriele, Gatti, Carlo, Lo Presti, Leonardo, Contreras-García, Julia
• Format: Journal Article
• Language: English
• Published: Weinheim WILEY-VCH Verlag 26.11.2012; WILEY‐VCH Verlag; Wiley Subscription Services, Inc
• Subjects: Aldehydes - chemistry; Benzopyrans - chemistry; Chemistry; Crystallography, X-Ray; Crystals; Electrons; Hydrogen Bonding; Mineralogy; Minerals; Models, Chemical; Molecular Conformation; Molecular Structure; noncovalent interactions; quantum chemistry; reduced density gradient; solid-state structures; X-ray diffraction
• ISSN: 0947-6539; 1521-3765
• DOI: 10.1002/chem.201201290

Non‐covalent interactions (NCI) define the rules underlying crystallisation, self‐assembly and drug–receptor docking processes. A novel NCI descriptor, based on the reduced electron density gradient (RDG), that enables easy visualisation of the zones of the electron density (ED) involved in either the supposedly attractive (dispersive, hydrogen bonding) or allegedly repulsive (steric) intermolecular interactions, was recently developed by Johnson et al. Here, it is applied for the first time to EDs derived from single‐crystal X‐ray diffraction data. A computer code handling both experimental and ab initio EDs in the RDG‐NCI perspective was purposely written. Three cases spanning a wide range of NCI classes were analysed: 1) benzene, as the prototype of stacking and weak CH⋅⋅⋅π interactions; 2) austdiol, a heavily functionalised fungal metabolite with a complex hydrogen‐bonding network; 3) two polymorphs of the heteroatom‐rich anti‐ulcer drug famotidine, with van der Waals and hydrogen‐bond contacts between N‐ and S‐containing groups. Even when applied to experimental EDs, the RDG index is a valuable NCI descriptor that can highlight their different nature and strength and provide results of comparable quality to ab initio approaches. Combining the RDG‐NCI study with Bader’s ED approach was a key step forward, as the RDG index can depict inherently delocalised interactions in terms of extended and flat RDG isosurfaces, in contrast to the bond path analysis, which is often bounded to a too localised and possibly discontinuous (yes/no) description. Conversely, the topological tool can provide quantitative insight into the simple, qualitative NCI picture offered by the RDG index. Hopefully, this study may pave the way to a deeper analysis of weak interactions in proteins using structural and ED information from experiment. A novel descriptor for non‐covalent interactions, based on the reduced electron density gradient (RDG), enables easy visualisation of the zones of electron density ρ(r) involved in intermolecular interactions, for example, the CH⋅⋅⋅π interactions in the benzene crystal (see figure), whereas the quantum theory of atoms in molecules (QTAIM) bond path descriptor singles out two specific atom–atom links.