In many cases, idealized crystal structure models cannot rationalize the actual properties of intermetallic compounds. For a realistic approach in materials research, microstructures and defects need to be taken into account. In case of clathrate compounds, particularly the intrinsic framework vacancies (denoted as Zintl defects) demand consideration. Consequently, clathrate research produces evidence that modern‐day structure chemistry involves the utilization of advanced X‐ray diffraction methods combined with elaborated bulk phase analyses, the investigation of phase relations, and the study of mutual interrelations in the triangle chemical bonding–structure–properties. Herein, we review some fundamental contributions to the specific defect chemistry of intermetallic clathrates. Binary systems, which combine E14 elements with electropositive metals, are characterized by a rich diversity of compounds. The emerging crystal structures may be divided into three characteristic branches and combinations thereof. The first branch consists of compounds with high content of the electropositive metal, and the crystal structures typically reveal motifs of ionic salts. A compound like Ba₂Si adopts the PbCl₂‐type of structure comprising isolated silicon atoms. The second branch is realized by Zintl phases, in which the quantity of formally transferred valence electrons of the electropositive metal atoms is insufficient to accomplish a noble gas configuration for isolated group 14 atoms. The resulting diversity of polyanions is characterized by covalent homoatomic bonding, while the interrelation of electron count and number of bonds is described by the 8‐N rule and the Zintl‐Klemm concept. A typical representative of this type is the butterfly anion Si₄^6– in the crystal structure of Ba₃Si₄.

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