The term matere bond has been recently used to refer to an attractive noncovalent interaction between any element of group 7 acting as an electrophile and any atom (or group of atoms) acting as a ...nucleophile. The utilization of metals such as σ-hole donors is starting to attract the attention of the scientific community. In this manuscript, a comparison between matere bonds and well-known σ-hole interactions (halogen and chalcogen bonds) is carried out using three X-ray structures, retrieved from the Cambridge structural database (CSD), and density functional theory calculations (DFT). The novelty of this work resides in the utilization of a neutral Re(VII) system as the matere bond donor and multivalent chalcogen and halogen donors. In fact, as far as our knowledge extends, the description of σ-hole interactions in Se(VI) is unprecedented in the literature. The σ-hole interactions in Re(VII), Se(VI) and Cl(VII) electron acceptors are analyzed and compared using several computational tools.
As(III) S‐adenosylmethionine methyltransferases, pivotal enzymes in arsenic metabolism, facilitate the methylation of arsenic up to three times. This process predominantly yields trivalent mono‐ and ...dimethylarsenite, with trimethylarsine forming in smaller amounts. While this enzyme acts as a detoxifier in microbial systems by altering As(III), in humans, it paradoxically generates more toxic and potentially carcinogenic methylated arsenic species. The strong affinity of As(III) for cysteine residues, forming As(III)‐thiolate bonds, is exploited in medical treatments, notably in arsenic trioxide (Trisenox®), an FDA‐approved drug for leukemia. The effectiveness of this drug is partly due to its interaction with cysteine residues, leading to the breakdown of key oncogenic fusion proteins. In this study, we extend the understanding of As(III)′s binding mechanisms, showing that, in addition to As(III)−S covalent bonds, noncovalent O⋅⋅⋅As pnictogen bonding plays a vital role. This interaction significantly contributes to the structural stability of the As(III) complexes. Our crystallographic analysis using the PDB database of As(III) S‐adenosylmethionine methyltransferases, augmented by comprehensive theoretical studies including molecular electrostatic potential (MEP), quantum theory of atoms in molecules (QTAIM), and natural bond orbital (NBO) analysis, emphasizes the critical role of pnictogen bonding in these systems. We also undertake a detailed evaluation of the energy characteristics of these pnictogen bonds using various theoretical models. To our knowledge, this is the first time pnictogen bonds in As(III) derivatives have been reported in biological systems, marking a significant advancement in our understanding of arsenic‘s molecular interactions.
This study advances our understanding of As(III) interactions in biological systems, revealing the important role of pnictogen bonding in As(III) S‐adenosylmethionine methyltransferases. The noncovalent As⋅⋅⋅O pnictogen bonds have been analyzed energetically and characterized studied using a variety of computational tools.
Unraveling the binding preferences involved in the formation of a supramolecular complex is key to properly understand molecular recognition and aggregation phenomena, which are of pivotal importance ...to biology. The halogenation of nucleic acids has been routinely carried out for decades to assist in their X-ray diffraction analysis. The incorporation of a halogen atom on a DNA/RNA base not only affected its electronic distribution, but also expanded the noncovalent interactions toolbox beyond the classical hydrogen bond (HB) by incorporating the halogen bond (HalB). In this regard, an inspection of the Protein Data Bank (PDB) revealed 187 structures involving halogenated nucleic acids (either unbound or bound to a protein) where at least 1 base pair (BP) exhibited halogenation. Herein, we were interested in disclosing the strength and binding preferences of halogenated A···U and G···C BPs, which are predominant in halogenated nucleic acids. To achieve that, computations at the RI-MP2/def2-TZVP level of theory together with state of the art theoretical modeling tools (including the computation of molecular electrostatic potential (MEP) surfaces, the quantum theory of "Atoms in Molecules" (QTAIM) and the non-covalent interactions plot (NCIplot) analyses) allowed for the characterization of the HB and HalB complexes studied herein.
Spontaneous self-assembly is one of the available synthetic routes to achieve structurally versatile and unique crystal complexes with selected metal-ligand combinations in the spirit of ...pseudohalides. In this endeavour, we designed a novel 1D coordination polymer (CP), (Cd)(Pb)(L)(η
1
-NCS)(η
1
-SCN)
n
(
1
), using a compartmental Salen ligand (H
3
L) in the presence of NaSCN. The characterization of the CP was accomplished using several spectroscopic techniques: MALDI-TOF, PXRD, SEM, EDX mapping, and single-crystal X-ray crystallography. The CP crystallizes in the monoclinic space group
P
2
1
/
c
with
Z
= 4. SCXRD reveals Cd(
ii
) and Pb(
ii
) metal ions fulfilled distorted square pyramidal and hemi-directed coordination spheres. Cd(
ii
) is placed in the inner N
2
O
2
and heavier Pb(
ii
) in the outer O
4
compartments of the de-protonated form of the ligand L
2−
. Supramolecular interactions in the intricate crystal structure produced attractive molecular architectures of the compound. The flexible aliphatic -OH pendent group coordinates with the Pb(
ii
) ions. This unique binding further elevates the supramolecular crystal topographies. The supramolecular interactions were authenticated by Hirshfeld surface analysis (HSA). The observation of the recurring unconventional tetrel bonds was rationalized by DFT calculations and surface plots of molecular electrostatic potential (MEP). In the 1D polymeric chain in the complex, the O-atom of the -OH groups shows a tetrel bonding interaction with the Pb atom. We have found that the combination of QTAIM/NCI and QTAIM/ELF plots helps reveal the nature of these contacts. Moreover, the QTAIM/ELF plot determines the donor-acceptor interaction between the O-atom and the Pb atom, establishing the σ-hole. Agreeably, the σ-hole interaction also helps Pb(
ii
) serve as a Lewis acid in the complex. Finally, spodium and tetrel bonds are formed, possible thanks to a hemi-directional coordination sphere of the Pb atoms in the polymer described.
We report σ-hole interaction/spodium/tetrel bonding and other non-covalent interactions in a heteronuclear Pb(
ii
)-Salen coordination polymer using DFT, HSA, QTAIM/NCI, and QTAIM/ELF plots. The non-covalent interactions predominantly drive the formation of extended architectures.
Four new heterometallic Cu(II)–U(VI) species, {(CuL1)(CH3CN)}UO2(NO3)2 (1), {(CuL2)(CH3CN)}UO2(NO3)2 (2), {(CuL3)(H2O)}UO2(NO3)2 (3), and UO2(NO3)2(H2O)2·2CuL4·H2O (4), were synthesized ...using four different metalloligands (CuL1, CuL2, CuL3, and CuL4, respectively) derived from four unsymmetrically dicondensed N,O-donor Schiff bases. Single-crystal structural analyses revealed that complexes 1, 2, and 3 have a discrete dinuclear Cu–UO2 core in which one metalloligand, CuL, is connected to the uranyl moiety via a double phenoxido bridge. Two chelating nitrate ions complete the octa-coordination around uranium. Species 4 is a cocrystal, where a uranyl nitrate dihydrate is sandwiched between two metalloligands CuL4 by the formation of strong hydrogen bonds between the H atoms of the coordinated water molecules to U(VI) and the O atoms of CuL4. Spectrophotometric titrations of these four metalloligands with uranyl nitrate dihydrate in acetonitrile showed a well-anchored isosbestic point between 300 and 500 nm in all cases, conforming with the coordination of CuL1, CuL2, CuL3, and the H-bonding interaction of CuL4 with UO2(NO3)2. This behavior of CuL4 was utilized to selectively bind metal ions (e.g., Mg2+, Ca2+, Sr2+, Ba2+, and La3+) in the presence of UO2(NO3)2·2H2O in acetonitrile. The formation of these Cu(II)–U(VI) species in solution was also evaluated by steady-state fluorescence quenching experiments. The difference in the coordination behavior of these metalloligands toward UO2(NO3)2(H2O)2 was studied by density functional theory calculations. The lower flexibility of the ethylenediamine ring and a large negative binding energy obtained from the evaluation of H bonds and supramolecular interactions between CuL4 and UO2(NO3)2(H2O)2 corroborate the formation of cocrystal 4. A very good linear correlation (r 2 = 0.9949) was observed between the experimental UO stretching frequencies and the strength of the equatorial bonds that connect the U atom to the metalloligand.
Analyses of the Cambridge Structural Database and theoretical calculations (PBE0-D3/def2-TZVP level, atoms-in-molecules, natural bond orbital studies) prove the formation of net attractive ...noncovalent interactions between group 5 elements and electron-rich atoms (neutral or anionic). These bondings are markedly different from coordination bonds formed by the same elements and possess the distinctive features of σ-hole interactions. The term erythroniumbond is proposed to denote these bonds. X-ray structures of vanadate-dependent bromoperoxidases show these interactions are present also in biological systems.
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.
Vanadium(V) derivatives, and to a lesser extent analogous compounds of niobium and tantalum, form attractive interactions with electron‐rich atoms (neutral or anionic). This bonding, given also by ...vanadate units in bromoperoxidase enzymes, is markedly different from the coordination bonds formed by the same elements, and possesses the distinctive features of σ‐hole interactions. The term “erythronium bond” is proposed to denote this kind bonding to honor Andrès Manuel del Río, who discovered vanadium. More information can be found in the Research Article by A. Frontera, G. Resnati, and co‐workers (DOI: 10.1002/chem.202302176).
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).
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