https://doi.org/10.15255/KUI.2024.036
Published: Kem. Ind. 74 (3-4) (2025) 117–137
Paper reference number: KUI-36/2024
Paper type: Original scientific paper
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Metavalent Bonds in Dimers of Metallic Elements within Biomacromolecules: Database-forming Approaches, Additionally Exemplified by Silver and Potassium Data

R. Kiralj

Abstract

Metallic homonuclear dimers exist in diverse forms, including as parts of biomacromolecular structures. The aim of this study was to identify all metallic elements forming such dimers in the Protein Data Bank (PDB), to rationalise dimer structure and bonding using various structural descriptors and statistical methods, and to support new findings with two additional studies on silver and potassium clusters. In total, 31 metals were identified as forming 565 dimers in crystal structures of biomacromolecules: s-block metals (Li, Na, Mg, K, Ca, Rb. Sr, Cs and Ba), transition metals (V, Mn, Fe, Co, Ni, Cu, Zn, Mo, Ru, Rh, Pd, Ag, Cd, Au and Hg), p-block metals (Ga, Tl and Pb), and lanthanides (La, Eu, Dy and Ho). These findings strongly suggest that any metal can form dimers within biomacromolecules. The identified dimers exhibit metavalent, or borderline metavalent/covalent, or metavalent/metallic bonding. In the PDB and other structural databases and literature sources, 761 silver clusters of all sizes were identified and analysed in terms of bonds per atom – bond length deviation relationship. Metavalent bonds or borderline metavalent/covalent or metavalent/metallic bonds exist in silver dimers and smaller clusters, whereas metallic bonding is predominant in larger clusters. Such or similar behaviour is expected for other metals. Partial atomic charge – radius relationship for 515 potassium clusters, from the PDB and other databases and sources, indicates that potassium dimers in biomacromolecules exhibit metavalent bonds or at least borderline metavalent/covalent or metavalent/metallic bonds, as demonstrated by the transferred electrons – shared electrons scatterplot. This behaviour is highly probable in other metals as well.

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Keywords

homonuclear metal dimers, biomacromolecular structures, metavalent bonding, statistical analysis, bonds per atom – bond length deviation relationship, atomic charge – radius relationship, transferred electrons – shared electrons relationship