Regium−π Bonds Involving Nucleobases: Theoretical Study and Biological Implications

Abstract

In this study, we provide crystallographic (Protein Data Bank (PDB) inspection) and theoretical (RI-MP2/def2-TZVP//PBE0-D3/def2-SVP level of theory) evidence of the involvement of nucleobases in Regium−π bonds (RgBs). This noncovalent interaction involves an electrophilic site located on an element of group 11 (Cu, Ag, and Au) and an electron-rich species (lone pair, LP donor, or π-system). Concretely, an initial PDB search revealed several examples where RgBs were undertaken involving DNA bases and Cu(II), Ag(I), and Au(I/ III) ions. While coordination positions (mainly at the N atoms of the base) are well known, the noncovalent binding force between these counterparts has been scarcely studied in the literature. In this regard, computational models shed light on the strength and directionality properties of the interaction, which was also further characterized from a charge-density perspective using Bader's "atoms in molecules" (AIM) theory, noncovalent interaction plot (NCIplot) visual index, and natural bonding orbital (NBO) analyses. As far as our knowledge extends, this is the first time that RgBs in metal−DNA complexes are systematically analyzed, and we believe the results might be useful for scientists working in the field of nucleic acid engineering and chemical biology as well as to increase the visibility of the interaction among the biological community.

Spodium Bonds Involving Methylmercury and Ethylmercury in Proteins: Insights from X-ray Analysis and Computations

“…In order to rationalize the nature of these interactions from an electrostatics point of view, we also computed the electrostatic potential surfaces of the alkyl Hg derivatives (Figure d), showing an electropositive belt around the Hg atoms with a similar electrostatic potential value (+18.2 and +16.3 kcal/mol for MeHg and EtHg, respectively) in line with that obtained for other linear transition-metal coordination complexes. , It is also important to note that although the common disposition of an SpB implies a σ-hole , (involving an antibonding metal–ligand orbital), the lineal geometry observed in the Hg coordination complexes studied herein precluded the presence of a σ-hole, thus resulting in the electropositive belt observed around the Hg atom (resembling a π-hole).…”

Wolfium bonds in homodimers of MX4Y (M = Mo, W; X = F, Cl, Br; Y = O, S, Se)

“…A diverse group of the transition metals can play a very similar role. Such bonding interactions have acquired tentative names such as regium (group 11), 25–29 spodium (group 12), 30–34 matere (group 7) 35–37 and osme (group 8) 38–40 bonds. As an example, the regium bond has been documented in the metal–DNA complexes, involving Cu( ii ), Ag( i ), Au( i ) and Au( iii ).…”

“…As an example, the regium bond has been documented in the metal–DNA complexes, involving Cu( ii ), Ag( i ), Au( i ) and Au( iii ). 29 Among the spodium bonds, both H-bonds and π-stacking interactions were observed as supplements in the solid state structure of Zn( ii ) with tetradentate secondary diamine ligands. 41 The properties of interactions in this co-crystal were evaluated by X-ray diffraction analysis and DFT calculations.…”

Supramolecular aggregation featuring Hg⋯S secondary-bonding interactions in crystals of mercury(ii) species augmented by computational chemistry calculations

“…under the aegis of regium bonding for interactions involving the coinage elements. [28][29][30] Further, chelate rings in metal complexes can behave in an analogous fashion as organic aromatic rings by accepting C-Y, e.g. Y = H and halogen, interactions 31,32 and forming π⋯π interactions.…”