In this study, a series of electron donor (–NH2, –NMe2 and –tBu) and electron-withdrawing substituents (–F, –CN and –NO2) were used to tune the nucleophilicity or electrophilicity of a series of ...square planar Ni2+, Pd2+ and Pt2+ malonate coordination complexes towards a pentafluoroiodobenzene and a pyridine molecule. In addition, Bader’s theory of atoms in molecules (AIM), noncovalent interaction plot (NCIplot), molecular electrostatic potential (MEP) surface and natural bond orbital (NBO) analyses at the PBE0-D3/def2-TZVP level of theory were carried out to characterize and discriminate the role of the metal atom in the noncovalent complexes studied herein. We hope that the results reported herein may serve to expand the current knowledge regarding these metals in the fields of crystal engineering and supramolecular chemistry.
In this manuscript substituent effects in several silicon tetrel bonding (TtB) complexes were investigated at the RI-MP2/def2-TZVP level of theory. Particularly, we have analysed how the interaction ...energy is influenced by the electronic nature of the substituent in both donor and acceptor moieties. To achieve that, several tetrafluorophenyl silane derivatives have been substituted at the meta and para positions by several electron donating and electron withdrawing groups (EDG and EWG, respectively), such as -NH
, -OCH
, -CH
, -H, -CF
and -CN substituents. As electron donor molecules, we have used a series of hydrogen cyanide derivatives using the same EDGs and EWGs. We have obtained the Hammett's plots for different combinations of donors and acceptors and in all cases we have obtained good regression plots (interaction energies vs. Hammet's σ parameter). In addition, we have used the electrostatic potential (ESP) surface analysis as well as the Bader's theory of atoms in molecules (AIM) and noncovalent interaction plot (NCI plot) techniques to further characterize the TtBs studied herein. Finally, a Cambridge Structural Database (CSD) inspection was carried out, retrieving several structures where halogenated aromatic silanes participate in tetrel bonding interactions, being an additional stabilization force of their supramolecular architectures.
The chalcogen bond has been recently defined by the IUPAC as the attractive noncovalent interaction between any element of group 16 acting as an electrophile and any atom (or group of atoms) acting ...as a nucleophile. Commonly used chalcogen bond donor molecules are divalent selenium and tellurium derivatives that exhibit two σ-holes. In fact, the presence of two σ-hole confers to the chalcogen bonding additional possibilities with respect to the halogen bond, the most abundant σ-hole interaction. In this manuscript, we demonstrate that selenoxides are good candidates to be used as σ-hole donor molecules. Such molecules have not been analyzed before as chalcogen bond donors, as far as our knowledge extends. The σ-hole opposite to the Se=O bond is adequate for establishing strong and directional ChBs, as demonstrated herein using the Cambridge structural database (CSD) and density functional theory (DFT) calculations. Moreover, the effect of the metal coordination of the selenoxide to transition metals on the strength of the ChB interaction has been analyzed theoretically. The existence of the ChBs has been further supported by the quantum theory of atoms in molecules (QTAIM) and the noncovalent interaction plot (NCIPlot).
Noncovalent interactions involving metals as electron acceptors are continuously under investigation. The term “matere bond” has been proposed to identify noncovalent donor–acceptor interactions ...where elements of group 7 of the periodic table play the role of the electrophilic site. Most of the works on matere bonds involve rhenium atoms usually in +7 oxidation state. This work emphasizes for the first time their importance in technetium derivatives in several oxidation states (+7, +6, +5, and +3). The Cambridge Structural Database (CSD) in combination with density functional theory (DFT) calculations are used to demonstrate the structure directing role of matere bonds in X-ray structures, even involving anion⋯anion interactions. Further characterization of the matere bonds is provided using Molecular Electrostatic Potential (MEP) surface calculations, the “Quantum Theory of Atoms in Molecules” (QTAIM), and Natural Bond Orbital (NBO) analyses. It should be emphasized that some types of matere bonds reported herein have not been previously described in literature.
In this manuscript, we have examined the CSD (Cambridge Structural Database) to investigate the relative ability of Te and I (in practice, the heaviest chalcogen and halogen atoms) in di- and ...tri-iododiorganyltellurium(IV) derivatives to establish σ-hole interactions. The geometry around the Te(IV) in this type of compound is trigonal bipyramidal where the stereoactive lone pair at Te(IV) occupies one of the equatorial positions. In the solid state, Te(IV) tends to form pseudo-octahedral coordination by establishing strong noncovalent interactions opposite to the two covalent bonds of the equatorial plane. Such contacts can also be classified as chalcogen bonds following the recommendation of the International Union of Pure and Applied Chemistry (IUPAC). Such contacts have been analyzed energetically in this work using density functional theory (DFT) calculations, rationalized using molecular electrostatic potential (MEP) surface analysis and characterized using a combination of the quantum theory of atoms in molecules (QTAIM) and noncovalent interaction plot (NCIplot) computational tools. Finally, the observation of halogen bonds and type I halogen···halogen contacts is also emphasized and compared to the chalcogen bonds. Energy decomposition analysis has also been performed to compare the physical nature of chalcogen, halogen and type I interactions.
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.
Some literature reports have shown the existence of short Hg(II)⋅⋅⋅d
M (M=Pd, Pt) contacts between linear Hg(II) and square planar d
M complexes that have been defined as heterometallophilic ...interactions. Linear L-Hg(II)-L complexes exhibit a π-hole or positive belt of electrostatic potential at the Hg atom, whereas late transition metals can serve as effective electron donors through their filled d
2 orbitals. This study provides compelling evidence that Hg(II)⋅⋅⋅d
M interactions should be more appropriately termed spodium bonds.
The Cover Feature vividly portrays the arrangement of distinct metallic atoms from various crystal structures, highlighting the extended contacts between mercury and palladium/platinum atoms. ...Initially identified as metallophilic interactions, these contacts may be more accurately described as spodium bonds. This reclassification stems from their characteristics, which more closely resemble non‐covalent donor‐acceptor interactions rather than traditional metallophilic contacts. More information can be found in the Research Article by Antonio Frontera and co‐workers.
