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A Protein Data Bank (PDB) survey has revealed noncovalent contacts involving Mn centres and protein residues. Their geometrical features are in line with the interaction between low electron density sites located along the Mn–O/N coordination bonds (σ-holes) and the lone pairs belonging to TYR, SER or HIS residues, known as a matere bond (MaB). Calculations at the PBE0-D3/def2-TZVP level of theory were used to investigate the strength and shed light on the physical nature of the interaction. We expect the results presented herein will be useful for those scientists working in the fields of bioinorganic chemistry, particulary in protein–metal docking, by providing new insights into transition metal⋯Lewis base interactions as well as a retrospective point of view to further understand the structural and functional implications of this key transition metal ion. [ABSTRACT FROM AUTHOR]

Metallophilic interactions, specifically argentophilic (Ag⋯Ag) and aurophilic (Au⋯Au) interactions, play a crucial role in stabilizing various molecular and solid-state structures. In this manuscript, we present a convenient method to estimate the strength of argentophilic and aurophilic interactions based on quantum theory of atoms in molecules (QTAIM) parameters evaluated at the bond critical points connecting the metal centres. We employ density functional theory (DFT) calculations and the QTAIM parameters to develop this energy predictor. To validate the reliability and applicability of our method, we test it using a selection of X-ray crystal structures extracted from the cambridge structural database (CSD), where argentophilic and aurophilic interactions are known to be significant in their solid-state arrangements. This method offers a distinct advantage in systems where multiple interactions, beyond metallophilic interactions, contribute to the overall stability of the structure. By employing our approach, researchers can distinctly quantify the strength of argentophilic and aurophilic interactions, facilitating a deeper understanding of their impact on molecular and solid-state properties. This method fills a critical gap in the existing literature, offering a valuable tool to researchers seeking to unravel the intricate interactions in metal-containing compounds. [ABSTRACT FROM AUTHOR]

Novel nitronyl nitroxides, namely 2-(3-iodoethynylphenyl)- and 2-(4-iodoethynylphenyl)-4,4,5,5-tetramethyl-imidazoline-3-oxyl-1-oxides, were prepared by condensation of appropriate aldehydes with 2,3-bis(hydroxylamino)-2,3-dimethylbutane followed by oxidative treatment with NaIO4. Crystal and molecular structures of the obtained paramagnets were studied by single-crystal X-ray diffraction. In the crystals, the radicals are assembled into zigzag chains in which the radical building blocks are linked by intermolecular I⋯N–O halogen bonding. Magnetic analyses revealed that in both nitronyl nitroxides, the radicals are weakly coupled. Nonetheless, spin–spin interactions in the 3-iodoethynyl isomer are antiferromagnetic, and the coupling is stronger than that in the 4-iodoethynyl derivative, in which the exchange interaction is ferromagnetic. DFT calculations in combination with MEP, NCIplot, and QTAIM analyses were used to evaluate and characterize the structure-directing halogen bonding interactions observed in the solid state of both compounds. [ABSTRACT FROM AUTHOR]

Computations at the PBE0-D3/def2-TZVP level of theory in conjunction with a Protein Data Bank (PDB) survey have provided first time evidence of favorable noncovalent interactions between ADP metavanadate (VO4) and ADP orthovanadate (VO5) and electron rich atoms. These involve a σ-hole present in the V atom and the lone pairs belonging to (i) protein residues (e.g., serine (SER), glutamate (GLU) or histidine (HIS)), (ii) backbone carbonyl groups and (iii) water molecules. A computational study has been carried out to rationalize the physical nature and directionality of the interaction in addition to its plausible biological role. The results reported herein are expected to have an impact in the fields of medicinal chemistry, bioinorganic chemistry and chemical biology. [ABSTRACT FROM AUTHOR]

Combining computations and X-ray structure analysis we have demonstrated that [Pt(CN4)]2− can behave as a Lewis acid inside an enzyme's cavity. The nature of a counterintuitive contact found between a catalytically active GLN residue belonging to a mitochondrial synthase and the Pt(II) center was investigated by combining molecular dynamics and quantum mechanics calculations. Results confirm the electron acceptor role of [Pt(CN4)]2−, serving as an inspiration for the design of biomolecular cages able to tweak the nucleophilic/electrophilic character of an organometallic compound. [ABSTRACT FROM AUTHOR]

Combining computations and X-ray structure analysis we have demonstrated that [Pt(CN4)]2− can behave as a Lewis acid inside an enzyme's cavity. The nature of a counterintuitive contact found between a catalytically active GLN residue belonging to a mitochondrial synthase and the Pt(II) center was investigated by combining molecular dynamics and quantum mechanics calculations. Results confirm the electron acceptor role of [Pt(CN4)]2−, serving as an inspiration for the design of biomolecular cages able to tweak the nucleophilic/electrophilic character of an organometallic compound. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

In recent years Pd(II) and Pt(II) cases have been reported wherein metals in square planar complexes were used as nucleophilic partners to construct supramolecular assemblies with electrophilic molecules like σ-hole and π-hole donors. The formation of such assemblies is based on the nucleophilicity and accessibility of the dz2 orbital (in group-10 elements) in the square-planar complexes. This opens new avenues in inorganic chemistry and crystal engineering as it enriches the current toolbox of noncovalent interactions and supramolecular synthons thus allowing the design of new types of architectures in the solid state. This manuscript reports a comprehensive theoretical study characterizing π-hole⋯dz2[MII] (M = group 10 element) interactions from an energetic point of view. Several computational tools based on the topology of the electron density are used. Examined systems had been identified by considering structures in the Cambridge Structural Database where this interaction was used to construct supramolecular assemblies. Several aromatic rings have been used, varying from π-basic to π-acid rings by adjusting the number of fluorine substituents. Moreover, the influence of metal⋯metal interactions on the nucleophilicity of the dz2 orbital has been studied using MEP surface analysis. The π-hole energies are moderately strong (from −5 to −10 kcal mol−1) and the crucial role of dispersion forces is revealed. [ABSTRACT FROM AUTHOR]

Herein we have computationally evaluated the relationship between Ag and Au nanoparticle (Ag/AuNP) size and π-surface extension in the formation of noncovalent complexes at the PBE0-D3/def2-TZVP level of theory. The NP-π interaction is known in supramolecular chemistry as a Regium-π bond (Rg-π), and differentiates from classical coordination bonds in strength and type of metal orbitals involved. In this study, the Rg-π complexes involved small Ag/AuNPs composed by 1 to 5 atoms and benzene, naphthalene and anthracene as π-systems, being characterized using several molecular modeling tools, including molecular electrostatic potential (MEP) calculations, energy decomposition analysis (EDA), quantum theory of atoms in molecules (QTAIM), non covalent interaction plot (NCIplot) and natural bonding orbital (NBO) methodologies. We believe the results reported herein will be useful for those scientists working in catalysis, molecular recognition and materials science fields, where structural-energetic relationships of weak interactions are crucial to achieve product selectivity, a particular molecular recognition mode or a specific molecular assembly.

Herein we have evidenced the formation of favorable π-hole Br···metal noncovalent interactions (NCIs) involving elements from groups 9, 11 and 12. More in detail, M (M = Co2+, Ni2+, Cu2+ and Zn2+) containing porphyrins have been synthesized and their supramolecular assemblies structurally characterized by means of single crystal X-ray diffraction and Hirshfeld surface analyses, revealing the formation of directional Br···M contacts in addition to ancillary hydrogen bond and lone pair-π bonds. Computations at the PBE0-D3/def2-TZVP level of theory revealed the π-hole nature of the Br···M interaction. In addition, the physical nature of these NCIs was studied using Quantum Chemistry methodologies, providing evidence of π-hole Spodium and Regium bonds in Zn2+ and Cu2+ porphyrins, in addition to unveiling the presence of  a π-hole for group 9 (Co2+). On the other hand, group 10 (Ni2+) acted as both electron donor and acceptor moiety without showing an electropositive π-hole. Owing to the underexplored potential of π-hole interactions in transition metal chemistry, we believe the results reported herein will be useful in supramolecular chemistry, organometallics, and solid-state chemistry by i) putting under the spotlight the π-hole chemistry involving first row transition metals and ii) unlocking a new tool to direct the self-assembly of metalloporphyrins., (© 2024 Wiley‐VCH GmbH.)

In this manuscript we evaluate the X-ray structure of five new pertechnetate derivatives of general formula [M(H 2 O) 4 (TcO 4 ) 2 ], M=Mg, Co, Ni, Cu, Zn (compounds 1-5) and one perrhenate compound Zn(H 2 O) 4 (ReO 4 ) 2 (6). In these complexes the metal center exhibits an octahedral coordination with the pertechnetate units as axial ligands. All compounds exhibit the formation of directional Tc⋅⋅⋅O Matere bonds (MaBs) that propagate the [M(H 2 O) 4 (TcO 4 ) 2 ], into 1D supramolecular polymers in the solid state. Such 1D polymers are linked, generating 2D layers, by combining additional MaBs and hydrogen bonds (HBs). Such concurrent motifs have been analyzed theoretically, suggesting the noncovalent σ-hole nature of the MaBs. The interaction energies range from weak (~ -2 kcal/mol) for the MaBs to strong (~ -30 kcal/mol) for the MaB+HB assemblies, where HB dominates. In case of M=Zn, the corresponding perrhenate Zn(H 2 O) 4 (ReO 4 ) 2 complex, has been also synthesized for comparison purposes, resulting in the formation of an isostructural X-ray structure, corroborating the structure-directing role of Matere bonds., (© 2024 The Authors. Chemistry - A European Journal published by Wiley-VCH GmbH.)

Some literature reports have shown the existence of short Hg(II)⋅⋅⋅d 8 [M] (M=Pd, Pt) contacts between linear Hg(II) and square planar d 8 [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 z 2 orbitals. This study provides compelling evidence that Hg(II)⋅⋅⋅d 8 [M] interactions should be more appropriately termed spodium bonds., (© 2023 The Authors. ChemPhysChem published by Wiley-VCH GmbH.)

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.

In recent years Pd(II) and Pt(II) cases have been reported wherein metals in square planar complexes were used as nucleophilic partners to construct supramolecular assemblies with electrophilic molecules like σ-hole and π-hole donors. The formation of such assemblies is based on the nucleophilicity and accessibility of the d z 2 orbital (in group-10 elements) in the square-planar complexes. This opens new avenues in inorganic chemistry and crystal engineering as it enriches the current toolbox of noncovalent interactions and supramolecular synthons thus allowing the design of new types of architectures in the solid state. This manuscript reports a comprehensive theoretical study characterizing π-hole⋯d z 2 [M II ] (M = group 10 element) interactions from an energetic point of view. Several computational tools based on the topology of the electron density are used. Examined systems had been identified by considering structures in the Cambridge Structural Database where this interaction was used to construct supramolecular assemblies. Several aromatic rings have been used, varying from π-basic to π-acid rings by adjusting the number of fluorine substituents. Moreover, the influence of metal⋯metal interactions on the nucleophilicity of the d z 2 orbital has been studied using MEP surface analysis. The π-hole energies are moderately strong (from -5 to -10 kcal mol -1 ) and the crucial role of dispersion forces is revealed.

Long range substituent effects in regium bonding interactions involving Au(I) linear complexes are investigated for the first time. The Au(I) atom is coordinated to two para-substituted pyridine ligands. The interaction energy (RI-MP2/def2-TZVP level of theory) of the π-hole regium bonding assemblies is affected by the pyridine substitution. The Hammett's plot representations for several sets of Lewis bases have been carried out and, in all cases, good regression plots have been obtained (interaction energies vs. Hammett's σ parameter). The Bader's theory of "atoms-in-molecules" has been used to evidence that the electron density computed at the bond critical point that connects the Au-atom to the electron donor can be used as a measure of bond order in regium bonding. Several X-ray structures retrieved from the Cambridge Structural Database (CSD) provide experimental support to the existence of π-hole regium bonding in [Au(Py) 2 ] + derivatives., (© 2022 Wiley-VCH GmbH.)